Potyvirus resistance genes and methods of use

ABSTRACT

Compositions and methods and for enhancing the resistance of plants to plant diseases caused by potyviruses are provided. The compositions comprise nucleic acid molecules encoding resistance (R) gene products and variants thereof and plants, seeds, and plant cells comprising such nucleic acid molecules. The methods for enhancing the resistance of a plant to plant disease caused by a potyvirus comprise introducing a nucleic acid molecule encoding an R gene product into a plant cell. Additionally provided are methods for using the plants in agriculture to limit plant disease.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a divisional of application Ser. No. 16/634,384, filed Jan. 27, 2020, which is the U.S. National Stage of International Application PCT/US2018/044108, filed Jul. 27, 2018, which designates the U.S. and was published by the International Bureau in English on Jan. 31, 2019, and which claims the benefit of U.S. Provisional Patent Application No. 62/538,020, filed Jul. 28, 2017, all of which are hereby incorporated herein in their entirety by reference.

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE

The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named 070294-0200SEQLST.TXT, created on Jan. 19, 2022, and having a size of 105 kilobytes, and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to the fields of gene isolation and plant improvement, particularly to enhancing the resistance of plants to plant disease through the use of disease resistance genes.

BACKGROUND OF THE INVENTION

Potato virus Y (PVY), a member of the Potyvirus genus (Potyviridae family), is the most economically important virus infecting potatoes, with tuber yield and quality losses reaching 85% (Valkonen (2007) “Potato viruses: economical losses and biotechnological potential,” in Potato biology and biotechnology, Viola et al., eds., Elsevier, San Diego, pp 619-641). PVY exists in nature as several distinct strains: the common (ordinary) group PVY^(O), the stipple streak group PVY^(C), a group of PVY^(Z) strains, the tobacco veinal necrosis group PVY^(N), and the tuber necrosis strain group PVY^(NTN). Additionally, a new group that does not induce tobacco veinal necrosis was identified and named PVY^(E) (Singh et al. (2008) Arch. Virol. 153: 1-13).

PVY is easily transmitted mechanically and can also be transmitted by over 40 aphid species in a non-persistent manner (Brunt (2001) “Potyviruses,” in Virus and virus-like diseases of potatoes and production of seed-potatoes, Loebenstein et al., eds., Kluwer Academic Publishers, London, pp. 77-84). Virus strains PVY^(O) and PVY^(C) usually induce mild symptoms of infection, e.g. leaf mosaic lesions, crinkling, leaf drop and dwarfing, while leaf symptoms of PVY^(N) and PVY^(N-Wilga) infection are barely noticeable. In addition to severe leaf symptoms, PVY^(NTN) infection leads to potato tuber necrotic ringspot disease (PTNRD) (Schubert et al. (2007) J. Virol. Methods 140: 66-74).

The pathogenicity of PVY is not limited to potato; other solanaceous crops such as pepper (Capsicum spp.), tomato (Solanum lycopersicum L.) and tobacco (Nicotiana tabacum L.) are affected by PVY as well. Potato and pepper as hosts seem to be selective for PVY strains, while it seems that tomato and tobacco can be infected with most PVY strains from potato and pepper (Aramburu (2006) Plant Pathol. 115:247-58).

Breeding of resistant cultivars is one of the most effective strategies to achieve protection against PVY (Świeżyński (1994) “Inheritance of resistance to viruses,” in Potato Genetics, Bradshaw and and Mackay, eds., CAB International, Wallingford, UK, pp. 339-363). In potato, there are two main types of resistance to PVY, the hypersensitive response (HR) and extreme resistance (ER) (Valkonen et al. (1996) Plant Breed. 115:433-38). The hypersensitive response to PVY is usually strain specific and may result in a range of necrotic reactions both in locally and systemically infected leaves (Valkonen et al. (1998) Phytopathology 88:1073-77). Genes conferring HR (Ny genes) are widely distributed in potato cultivars (Ruiz de Galarreta et al. (1998) Potato Res. 41:57-68). In some cases, however, hypersensitivity may be ineffective for restriction of PVY in plants (Vidal et al. (2002) Mol. Plant Microbe Interact. 15:717-27). ER genes are broad-spectrum and confer strong and durable resistance, characterized by lack of visible symptoms after inoculation (Flis et al. (2005) Mol. Breed. 15:95-101).

Resistance genes against PVY infection had been introduced into potato cultivars from many sources (Table 1), as was summarized by van Eck et al. ((2017) Theor. Appl. Genet. 130:515-528)). Some of these genes, for example Ry from Solanum stoloniferum (also referred to as “Ry_(sto)”), were introduced into multiple European cultivars and were shown to confer durable resistance against multiple PVY strains. Ry_(sto) and Ry-f_(sto), another PVY resistance gene from S. stoloniferum, are widely used in the breeding of potato varieties for resistance to PVY (Flis et al. (2005) Mol. Breed. 15:95-101; Song et al. (2005) Theor. Appl. Genet. 111:879-887).

TABLE 1 Resistance Loci Against PVY Infection Ancestral Locus Chromosome germplasm References Ncspl 4 S. sparsipilum Moury et al. (2011) Mol. Plant-Microbe Interact. 24: 787-797 Nytbr 4 S. tuberosum Celebi-Toprak et al. (2002) Theor. Appl. Genet. 104: 669- 674 Ry_(chc) 9 S. chacoense Hosaka et al. (2001) Am. J. Potato Res. 78: 191-196 Sato et al. (2006) Euphytica 149: 367-372 Ny-1 9 cv. Rywal Szajko et al. (2008) Theor. Appl. Genet. 116: 297-303 Ny-Smira  9 cv. Sarpo Mira Tomczyńska et al. (2014) Mol. Breed. 34: 471-480 Ry_(adg) 11 group andigena Hämäläinen et al. (1997) Theor. Appl. Genet. 94: 192-197 Hämäläinen et al. (1998) Theor. Appl. Genet. 96: 1036-1043 Ny-2 11 cv. Romula Szajko et al. (2014) Mol. Breed. 34: 267-271 Ry_(sto) 11 S. stoloniferum Brigneti et al. (1997) Theor. Appl. Genet. 94: 198-203 Ry-f_(sto) 12 S. stoloniferum Flis et al. (2005) Mol. Breed. 15: 95-101 Song et al. (2005) Theor. Appl. Genet. 111: 879-887

There is a high demand for new solanaceous crop plant varieties comprising strong and durable resistance genes against PVY to limit the economic losses caused by this devastating plant pathogen. However, producing such new solanaceous crop plant varieties by traditional plant breeding methods can be both laborious and time consuming. More rapid methods involving the introduction of cloned resistance genes into existing elite germplasm via genetic engineering can be used to produce new solanaceous crop plant varieties, but such rapid methods depend on the availability of cloned resistance genes. Unfortunately, none of the genes conferring effective HR or ER-type of resistance have yet been reported to have been cloned (Vidal et al. (2002) Mol. Plant Microbe Interact. 15:717-27; Kim et al. (2017) New Phytol. 213:886-899). The available of cloned resistance genes against PVY would enable plant breeders to produce more rapidly new solanaceous crop plant varieties comprising, not only multiple resistance genes against multiple strains of PVY, but also one or more resistance genes against other important plant pathogens such as, for example, Phytophthora infestans, the causal agent of late blight of potatoes and tomatoes.

BRIEF SUMMARY OF THE INVENTION

The present invention provides nucleic acid molecules of resistance (R) genes that are capable of conferring to a plant resistance to at least one potyvirus that is known to cause a plant disease in the plant. In certain embodiments of the invention, the nucleic acid molecules of R genes are capable of conferring to a plant, particularly a solanaceous plant, resistance to at least one strain of Potato virus Y (PVY) and/or Potato virus A (PVA) that is known to cause a plant disease in the plant. Preferably, such nucleic acid molecules are capable of conferring to a plant enhanced resistance to multiple strains of PVY and/or PVA including, for example, at least two, three, four, five, or more strains of PVY and/or PVA. In one embodiment, the present invention provides nucleic acid molecules of an R gene, which is referred to herein as c630, and its variants including, for example, orthologs, and other naturally and non-naturally occurring variants of c630. In another embodiment, the present invention provides nucleic acid molecules of an R gene, which is referred to herein as c516, and its variants including, for example, orthologs and other naturally and non-naturally occurring variants of c516.

The present invention further provides plants, plant cells, and seeds comprising in their genomes one or more heterologous polynucleotides of the invention. The heterologous polynucleotides comprise a nucleotide sequence encoding a resistance (R) protein of the present invention. Such R proteins are encoded by the R genes of the present invention, particularly c630 and c516, their respective orthologs and other naturally and non-naturally occurring variants of c630 and c516. In a preferred embodiment, the plants and seeds are transgenic solanaceous plants and seeds that have been transformed with one or more heterologous polynucleotides of the invention. Preferably, such solanaceous plants comprise enhanced resistance to at least one strain of PVY and/or PVA that is known to cause a plant disease in a solanaceous plant, when compared to the resistance of a control plant that does not comprise the heterologous polynucleotide. More preferably, such solanaceous plants comprise enhanced resistance to two, three, four, or more strains of PVY and/or PVA that a known to cause a plant disease in a solanaceous plant, when compared to the resistance of a control plant that does not comprise the heterologous polynucleotide. Solanaceous plants of the invention include, but are not limited to, domesticated solanaceous plants including, for example, domesticated varieties of potato, tomato, pepper, and tobacco.

The present invention provides methods for enhancing the resistance of a plant to at least one potyvirus that is known to cause a plant disease in the plant. In certain embodiments of the invention, the methods involve enhancing the resistance of a plant, particularly a solanaceous plant, to a plant disease caused by at least one strain of PVY and/or PVA. Such methods comprise introducing into at least one plant cell a heterologous polynucleotide comprising a nucleotide sequence of an R gene of the present invention. Preferably, the heterologous polynucleotide or part thereof is stably incorporated into the genome of the plant cell. The methods can optionally further comprise regenerating the plant cell into a plant that comprises in its genome the heterologous polynucleotide. Preferably, such a plant comprises enhanced resistance to a plant disease caused by at least one potyvirus, particularly at least one strain of PVY and/or PVA, relative to the resistance of a control plant not comprising the heterologous polynucleotide. More preferably, such a plant comprises enhanced resistance to plant disease(s) caused by at least two, three, four, five, or more strains of PVY and/or PVA, relative to the resistance of a control plant not comprising the heterologous polynucleotide. In the certain embodiments, the plant produced by the methods of the present invention comprises enhanced resistance to at least one potyvirus that is not PVY or PVA. In the certain embodiments, the plant produced by the methods of the present invention comprises enhanced resistance to at least one least one strain of PVY and/or at least one least one strain of PVA, and further comprises enhanced resistance to at least one additional potyvirus, wherein the additional potyvirus is not PVY or PVA.

The present invention additionally provides methods for identifying a solanaceous plant that comprises an R gene for a plant disease caused by at least one strain of PVY and/or PVA. The methods comprise detecting in the solanaceous plant the presence of c630, c516, or both c630 and c516.

Methods of using the plants of the present invention in agricultural crop production to limit plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one other potyvirus are also provided. The methods comprise planting a plant (e.g. a seedling), a tuber, or a seed of the present invention, wherein the plant, tuber, or seed comprises at least one R gene nucleotide sequence of the present invention. The methods further comprise growing a plant under conditions favorable for the growth and development of the plant, and optionally harvesting at least one fruit, tuber, leaf, or seed from the plant.

Additionally provided are plants, plant parts, seeds, plant cells, other host cells, expression cassettes, and vectors comprising one or more of the nucleic acid molecules of the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B are graphs illustrating levels of PVY mRNA after infection of N. benthamiana leaves transiently expressing candidate contigs. For the results shown in FIG. 1A, the third leaves of N. benthamiana plants were separately infiltrated with the vector pICSLUS0003::35S overexpressing candidate contig c124_1, c124_2, c516, c630, c908, c1459 or c660, or with an empty vector (negative control). Twenty-four hours later the leaves were inoculated with PVY^(NTN) (isolate NIB-NTN). Seven days after the PVY inoculation, mRNA was isolated from upper, non-inoculated leaves and PVY mRNA levels were quantified with quantitative RT-PCR. Two constructs, c630 and c516, showed significant reduction of viral mRNA levels. Expression of candidate c630 from pICSLUS0001 vector under control of native regulatory elements, resulted in a similar reduction of viral mRNA level as for pICSLUS0003::35S::c630 construct. For the results shown in FIG. 1B, the experiment was performed as described above for FIG. 1A with two additional candidate genes, c359 and c692, and with an empty vector as a negative control. There was no statistically significant difference in viral mRNA levels between these candidate contigs and the negative control. For both FIGS. 1A and 1B, the experiments were performed on 3-10 plants for each construct and the points on the graph represent mRNA levels in independent plants. For some constructs, the experiment was repeated two to three times; different point shapes on the graph represent plants from different experiments.

FIG. 2. is a photographic illustration of the HR developed after infiltration of c630 into N. benthamiana plants systemically infected with PVY. Four-week-old N. benthamiana plants systemically infected with PVY^(NTN) (NIB-NTN, left) or PVX (right) were infiltrated with the vector pICSLUS0003::355 overexpressing c630 or c516 (not shown) candidate genes, or Rx control gene. Only the infiltration of c630 into PVY-infected plants resulted in a strong HR at 3 days post inoculation (dpi), similar to the one in the control experiment in which Rx was infiltrated into PVX-carrying plants (right). The photographs were taken at 5 dpi.

FIG. 3. is a photographic illustration of the HR response after PVY inoculation in stable transgenic N. tabacum plants transformed with 35S::c630. Seven-week-old N. tabacum 35S transgenic and wild-type (WT) control, N. tabacum plants were inoculated with PVY^(NTN) (isolate NIB-NTN). The HR was observed only on N. tabacum 35S::c630 inoculated leaves at 3 dpi. WT control plants remained symptomless. The photographs were taken at 7 dpi.

FIGS. 4A-4B are photographic illustrations of systemic, non-inoculated leaves of N. tabacum plants after 14 days after inoculation with PVY. FIG. 4A shows leaves from N. tabacum plants transformed with 35S::c630. FIG. 4B shows leaves from WT control, N. tabacum plants. Seven-week-old N. tabacum 35S::c630 transgenic plants and WT control, N. tabacum plants were inoculated with PVY^(NTN) (isolate NIB-NTN). While typical symptoms of PVY infection were observed on WT control plants (FIG. 4B), lines 630A, 630B and 630E transformed with 35S::c630 did not show any symptoms of infection. FIG. 4A shows line 630A which is representative of the other two transformed lines. The photographs were taken at 14 dpi.

FIG. 5. is a photographic illustration of systemic, non-inoculated leaves of transgenic 35S::c630 N. tabacum plants showing partial resistance to PVY at 14 dpi. Seven-week-old N. tabacum transgenic 35S::c630 plants were inoculated with PVY^(NTN) as above. Lines C, D, F, G and H showed severe infections symptoms on upper leaves, leading eventually to systemic necrotization and plant death. Only line 630G is shown for the purpose of illustration.

FIGS. 6A-6D is a multi-panel figure that provides graphical illustrations of PVY mRNA levels and the expression levels of candidate gene c630 in stably transformed plants following PVY inoculation. FIGS. 6A and 6C are graphs illustrating levels of PVY mRNA after infection of stable transgenic N. tabacum plants transformed with a 35S::c630 construct, and FIGS. 6B and 6D are graphs showing the expression of candidate gene c630 in the same plants. Seven-week-old N. tabacum 35S::c630 transgenic and WT control, N. tabacum plants were inoculated with PVY^(NTN) as described above or mock treated with inoculation buffer. Seven and 14 days after PVY inoculation, mRNA was isolated from upper, non-inoculated leaves. PVY mRNA levels and the expression of candidate gene c630 were quantified with quantitative RT-PCR. The high expression of the candidate gene c630 (FIG. 6B) correlated with lack of PVY mRNA (FIG. 6A) for lines A, B and E in stable transgenic T0 plants. Resistant lines A and E were again tested in the T1 generation, confirming the results from T0 (FIGS. 6C, 6D). Line 630G (susceptible), for which the expression of c630 was not detected, had PVY mRNA levels similar to control line c908B carrying a non-functional paralog (FIGS. 6C, 6D).

FIGS. 7A-7B is a multi-panel figure that provides graphical illustrations of PVY mRNA levels and the expression levels of candidate gene c630 in stable transgenic N. tabacum plants transformed with the c630 gene under the control of its native regulatory elements following PVY inoculation. Seven-week-old N. tabacum 35S::c630 transgenic and WT control, N. tabacum plants were inoculated with PVY^(NTN) as described above. Seven and 14 days after PVY inoculation, mRNA was isolated from upper, non-inoculated leaves. PVY mRNA levels and the expression of candidate gene c630 were quantified with quantitative RT-PCR. In lines E, G, H and M, high expression of the candidate gene c630 (FIG. 7B) correlated with lack of PVY mRNA (FIG. 7A) in stable transgenic T0 plants.

FIG. 8. is a photographic illustration of PVY-inoculated leaves of transgenic 35S::c630 and wild type (WT) S. tuberosum cv. Russet Burbank plants showing an ER-type of response. Four-week-old transgenic potato plants cv. Russet Burbank carrying construct 35S::c630, and WT control plants were inoculated with PVY^(NTN) (NIB-NTN). Chlorosis were observed on inoculated leaves of WT plants since 11 dpi (right leaf). Transgenic plants (left leaf) carrying construct 35S::c630 remained symptomless for at least 3 weeks post inoculation (wpi).

FIGS. 9A-9B. is a multi-panel figure that provides graphical illustrations of PVY mRNA levels and the expression levels of candidate gene c630 in stable, transgenic S. tuberosum cv. Russet Burbank plants transformed with the 35S::c630 construct following inoculation with PVY. Seven-week-old potato 35S::c630 transgenic and WT Russet Burbank plants were inoculated with PVY^(NTN) as described above. Three weeks after PVY inoculation, mRNA was isolated from upper, non-inoculated leaves. PVY mRNA levels, and the expression of candidate gene c630 were quantified with quantitative RT-PCR. In all tested lines (A, B, C and D), expression of the candidate gene c630 (FIG. 9B) correlated with lack of PVY mRNA (FIG. 9A) in stable transgenic T0 plants. The presence of PVY mRNA was only detected in WT control plants. The experiment was performed on three plants for line 630A and 630B, on two plants for line 630D, and on one plant for line 630C.

FIGS. 10A-10B is a multi-panel figure that provides graphical illustrations of PVY mRNA levels (FIG. 10A) and the expression levels of the c630 gene (FIG. 10B) in stable, transgenic S. tuberosum cv. Maris Piper plants transformed with the c630 gene construct comprising the native c630 5′- and 3′-regulatory elements. Four-week-old transgenic potato plants cv. Maris Piper carrying the c630 construct were inoculated with PVY^(NTN). Three weeks after PVY inoculation, mRNA was isolated from upper, non-inoculated leaves. In all tested lines (A, E, I, M and O), expression of the candidate gene c630 (FIG. 10B) correlated with lack of PVY mRNA (FIG. 10A) in stable transgenic T0 plants. The presence of PVY mRNA was only detected in WT control plants. The PVY mRNA levels and the expression of Rysto-630 were quantified with qPCR, relative to the expression of the EF1 and Sec3 reference genes and expressed as means±SD calculated from three biological replicates per plant line.

FIG. 11 is a photographic illustration of the HR response after PVA inoculation in stable transgenic N. tabacum plants transformed with 35S::c630. Seven-week-old N. tabacum 35S transgenic and wild-type (WT) control, N. tabacum plants were inoculated with PVA (strain SASA). The HR was observed only on N. tabacum 35S::c630 inoculated leaves (leaf leaf) at 7 dpi. WT control plants remained symptomless (right leaf). The photographs were taken at 10 dpi.

SEQUENCE LISTING

The nucleotide and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three-letter code for amino acids. The nucleotide sequences follow the standard convention of beginning at the 5′ end of the sequence and proceeding forward (i.e., from left to right in each line) to the 3′ end. Only one strand of each nucleotide sequence is shown, but the complementary strand is understood to be included by any reference to the displayed strand. The amino acid sequences follow the standard convention of beginning at the amino terminus of the sequence and proceeding forward (i.e., from left to right in each line) to the carboxy terminus.

SEQ ID NO: 1 sets forth the nucleotide sequence of the R gene, c630.

SEQ ID NO: 2 sets forth the amino acid sequence C630-SV1, the R protein encoded by splice variant 1 of c630.

SEQ ID NO: 3 sets forth the nucleotide sequence of the coding region of the cDNA of splice variant 1 of c630. If desired, a stop codon (e.g. TAA, TAG, TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 3. The native stop codon of this cDNA is TGA.

SEQ ID NO: 4 sets forth the amino acid sequence C630-SV2, the R protein encoded by splice variant 2 of c630.

SEQ ID NO: 5 sets forth the nucleotide sequence of the coding region of the cDNA of splice variant 2 of c630. If desired, a stop codon (e.g. TAA, TAG, TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 5. The native stop codon of this cDNA is TGA.

SEQ ID NO: 6 sets forth the nucleotide sequence of the R gene, c516.

SEQ ID NO: 7 sets forth the amino acid of the R protein encoded by c516 SEQ ID NO: 8 sets forth the nucleotide sequence of the coding region of the cDNA of c516. If desired, a stop codon (e.g. TAA, TAG, TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 8. The native stop codon of this cDNA is TAG.

SEQ ID NO: 9 sets forth the nucleotide sequence of the CaMV 35S promoter::c630 construct that used in to transformed plants as described below in the Examples.

SEQ ID NO: 10 sets forth the nucleotide sequence of the portion of SEQ ID NO: 9 that corresponds to a fragment of c630 (SEQ ID NO: 1) comprising the coding region.

SEQ ID NO: 11 sets forth the nucleotide sequence of the CaMV 35S promoter::c516 construct that used to transform plants as described below in the Examples below.

SEQ ID NO: 12 sets forth the nucleotide sequence of the s portion of SEQ ID NO: 11 that corresponds to a fragment of c516 (SEQ ID NO: 6) comprising the coding region.

SEQ ID NO: 13 sets forth the nucleotide sequence of the c630 native construct (i.e. native regulatory elements) that was used to transform plants as described in the Examples below.

DETAILED DESCRIPTION OF THE INVENTION

The present inventions now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the inventions are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Like numbers refer to like elements throughout.

Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

The present invention relates to the isolation of plant resistance (R) genes, particularly R genes that confer upon a solanaceous plant resistance to plant disease(s) caused by one or more strains of the potyviruses, Potato virus Y (PVY) and/or Potato virus A (PVA). As disclosed hereinbelow, an R gene, referred to herein as c630, was isolated from a diploid potato (Solanum tuberosum) mapping population obtained from a cross between PVY-resistant, heterozygous dihaploid clone dH Alicja and susceptible, diploid clone 83-3121 using a method that combined bulked segregant analysis and R gene enrichment and sequencing (RenSeq) to rapidly identify candidate genes encoding nucleotide binding-leucine rich repeat (NLR) proteins.

dH Alicja was selected as the source of PVY resistance because dH Alicja is known to comprise in its genome the resistance gene Ry_(sto) which confers extreme resistance (ER) to multiple strains of PVY. As described in additional detail below, Ry_(sto) was introgressed into the S. tuberosum genome via an interspecific cross with a Solanum stoloniferum plant comprising in its genome Ry_(sto). While it is believed that the results disclosed hereinbelow in the Examples conclusively demonstrate that c630 is Ry_(sto), the present invention does not depend on c630 being Ry_(sto) or Ry-f_(sto), or even on c630 being derived from DNA in the genome of dH Alicja that was introgressed from the genome of S. stoloniferum.

Moreover, it is recognized that there are at least two sources of the Ry resistance trait or gene that is derived from Solanum stoloniferum. One Ry resistance trait is derived from an S. stoloniferum line of Russia origin that is fertile and has the designation Ry-f_(sto) (“f” for fertile). The other Ry resistance trait is derived from an S. stoloniferum line of German origin that is male sterile and has the designation Ry_(sto). It is recognized that dH Alicja, which is the source of c630 of the present invention, comprises the Ry_(sto) resistance trait that is derived from the male sterile, S. stoloniferum line of German origin.

Because the Ry-f_(sto) and Ry_(sto) resistance traits map to the same site on chromosome 12 and potato plants comprising either Ry-f_(sto) or Ry_(sto) have the same PVY resistance phenotype, Ry-f_(sto) and Ry_(sto) may be different alleles of one Ry gene or even the same allele of one Ry gene. Alternatively, Ry-f_(sto) and Ry_(sto) may be separate Ry genes that are tightly linked. Nevertheless, the methods and compositions of the present invention do not depend on whether or not Ry-f_(sto) and Ry_(sto) are different alleles of one Ry gene, the same allele of one Ry gene, or are separate Ry genes.

The present invention provides nucleic acid molecules comprising the nucleotide sequences of R genes, particularly the nucleotide sequences of c630 and other naturally occurring (e.g. orthologs and allelic variants) and synthetic or artificial (i.e. non-naturally occurring) variants thereof. As used herein, such nucleic acid molecules are referred to herein as “c630 nucleic acid molecules”. Likewise, the nucleotide sequences of c630 and other naturally occurring (e.g. orthologs and allelic variants) and synthetic or artificial (i.e. non-naturally occurring) variants thereof are referred to herein as “c630 nucleotide sequences”.

The present invention further provides nucleic acid molecules comprising the nucleotide sequences of R genes, particularly the nucleotide sequences of c516 and other naturally occurring (e.g. orthologs and allelic variants) and synthetic or artificial (i.e. non-naturally occurring) variants thereof. As used herein, such nucleic acid molecules are referred to herein as “c516 nucleic acid molecules”. Likewise, the nucleotide sequences of c516 and other naturally occurring (e.g. orthologs and allelic variants) and synthetic or artificial (i.e. non-naturally occurring) variants thereof are referred to herein as “c516 nucleotide sequences”. It is recognized that, as used herein, the term “R genes of the present invention” encompasses both the c630 nucleic acid molecules and the c516 nucleic acid molecules described above.

The c630 nucleotide sequences and the c516 nucleotide sequences of the present invention are nucleotide sequences of R genes, which are also referred to herein as R gene nucleotide sequences. Preferably, such nucleotide sequences of R genes encode R proteins. c630 nucleotide sequences and c516 nucleotide sequences of the invention include, but not limited to: the nucleotide sequences of the wild-type or native c630 and c516 genes comprising a native promoter and the native 3′ adjacent region comprising the coding region; cDNA sequences; and nucleotide sequences comprising only the coding region. Examples of such c630 nucleotide sequences include the nucleotide sequences set forth in SEQ ID NOS: 1, 3, 5, 9, 10, and 13, and variants thereof. Examples of such c516 nucleotide sequences include the nucleotide sequences set forth in SEQ ID NOS: 6, 8, 11, and 12, and variants thereof. In embodiments in which the native c630 or c516 gene promoter is not used to drive the expression of the nucleotide sequence encoding the R protein, a heterologous promoter can be operably linked a nucleotide sequence encoding an R protein of the invention to drive the expression of nucleotide sequence encoding an R protein in a plant.

Preferably, the R proteins encoded by the c630 nucleotide sequences and the c516 nucleotide sequences of the invention are functional R proteins, or part(s), or domain(s) thereof, which are capable of conferring on a plant, particularly a solanaceous plant, comprising the R protein, enhanced resistance to a plant disease caused by at least one strain of PVY and/or PVA. PVY strains include, but are not limited to, PVY^(O), PVY^(C), PVY^(Z), PVY^(N), PVY^(NTN), PVY^(N-Wilga) and PVY^(E). PVA strains include, but are not limited to, PVA-1, PVA-2, PVA-3 which correspond to isolates PVA-U, PVA-M, and PVA-B11, respectively (Valkonen et al. (1995) Plant Dis. 79:748-753.) Other PVA strains include, for example, PVA-SASA and PVA-X Bonin.

In certain preferred embodiments, the R proteins of the present invention comprise broad-spectrum resistance to multiple strains of PVY and/or PVA and include, for example, C630-SV1 (SEQ ID NO: 2) and C630-SV2 (SEQ ID NO: 4), the two R proteins encoded by c630 (SEQ ID NO: 1). Such R proteins are encoded by the c630 nucleotide sequences set forth in SEQ ID NOS: 1, 3, and 5 and variants thereof. In certain other preferred embodiments, the R proteins of the present invention comprise broad-spectrum resistance to multiple strains of PVY and include, for example, C516 (SEQ ID NO: 7), the R protein encoded by c516 (SEQ ID NO: 6). Such R proteins are encoded by the c516 nucleotide sequences set forth in SEQ ID NOS: 6, 8, 11, and 12, and variants thereof.

The present invention further provides plants comprising a heterologous polynucleotide which comprises an R gene nucleotide sequence of the present invention. Preferably, such an R gene nucleotide sequence encodes a full-length R protein of the present invention, or at least a functional part(s) or domain(s) thereof. In some embodiments, such a heterologous polynucleotide of the present invention is stably incorporated into the genome of the plant, and in other embodiments, the plant is transformed by a transient transformation method and the heterologous polynucleotide is not stably incorporated into the genome of the plant.

In other embodiments, a plant comprising a heterologous polynucleotide which comprises an R gene nucleotide sequence of the present invention is produced using a method of the present invention that involves genome editing to modify the nucleotide sequence of a native or non-native gene in the genome of the plant. The native or non-native gene comprises a nucleotide sequence that is different from (i.e. not identical to) an R gene nucleotide sequence of the present invention, and after modification by methods disclosed in further detail hereinbelow, the modified native or non-native gene comprises an R gene nucleotide sequence of the present invention. Generally, such methods comprise the use of a plant comprising in its genome a native or non-native gene wherein the native or non-native gene comprises a nucleotide sequence that is homologous to an R gene nucleotide sequence of the present invention and further comprises introducing into the plant a nucleic acid molecule comprising at least part of an R gene nucleotide sequence of the present invention. Preferably, a nucleotide sequence of native or non-native gene comprises about 70%, 75% 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater nucleotide sequence identity to at least one R gene nucleotide sequence of the present invention. Such a native or non-native gene can be, for example an R gene, or a non-functional homolog of such an R gene that is not, or is not known to be, capable of conferring to a plant, resistance to a plant disease. It is recognized that a plant produced by genome engineering as disclosed herein is a stably transformed plant when the native or non-native gene that is modified is stably incorporated in the genome of the plant.

Methods for both the stable and transient transformation of plants and genome editing are disclosed elsewhere herein or otherwise known in the art. In one embodiment of the invention, the plants are stably transformed potato or tomato plants comprising a heterologous polynucleotide of the present invention stably incorporated into their respective genomes and further comprising enhanced resistance to plant disease caused by at least one strain of PVY, enhanced resistance to plant disease caused by at least one strain of PVA, and/or enhanced resistance to plant disease caused by at least other potyvirus (i.e. a potyvirus other than PVY or PVA). In another embodiment of the invention, the plants are stably transformed potato or tomato plants comprising a heterologous polynucleotide of the present invention stably incorporated into their respective genomes and further comprising enhanced resistance to plant disease caused by at least two, three, four, five, six or more strains of PVY and/or PVA, and optionally comprise enhanced resistance to at least one other potyvirus.

In certain embodiments, a plant of the invention comprises a heterologous polynucleotide which comprises a nucleotide sequence encoding an R protein of the present invention and a heterologous promoter that is operably linked for expression of the nucleotide sequence encoding an R protein. The choice of heterologous promoter can depend on a number of factors such as, for example, the desired timing, localization, and pattern of expression as well as responsiveness to particular biotic or abiotic stimulus. Promoters of interest include, but are not limited to, pathogen-inducible, constitutive, tissue-preferred, wound-inducible, and chemical-regulated promoters.

In certain embodiments of the invention, the plant of the invention, particularly a solanaceous plant, can comprise one, two, three, four, five, six, or more nucleotide sequences encoding an R protein. Typically, but not necessarily, the two or more R proteins will be different from each other. For the present invention, an R protein is different from another R protein when the two R proteins have non-identical amino acid sequences. In some embodiments of the invention, a solanaceous plant can comprise a nucleotide sequence encoding both C630-SV1 and C630-SV2. In other embodiments, a solanaceous plant can comprise a first nucleotide sequence encoding C630-SV1 and a second nucleotide sequence encoding C630-SV2. In yet other embodiments, a solanaceous plant can comprise a first nucleotide sequence encoding both C630-SV1 and C630-SV2 and a second nucleotide sequence encoding C516. In still yet other embodiments, a solanaceous plant can comprise a first nucleotide sequence encoding C630-SV1, a second nucleotide sequence encoding C630-SV2, and a third nucleotide sequence encoding C516.

One or more nucleic acid molecules comprising an R genes nucleotide sequences of the present invention can be combined in a single plant, particularly solanaceous plant, with any one or more other R genes for plant disease caused by PVY and/or PVA, or for any other plant disease caused by a plant pathogen such as, for example, late blight caused by Phytophthora infestans. Other R genes for plant disease caused by PVY include, but are not limited to, Ncspl, Nytbr, Ry_(chc), Ny-1, Ny-Smira, Ry_(adg), and Ny-2 (see Table 1 above). Late blight R genes, which are also referred to as Rpi (i.e. Resistance to Phytophthora infestans) genes, can be combined in single solanaceous plant (e.g. a potato plant) comprising at least one R gene nucleotide sequence of the present invention include, but are not limited to, the following cloned Rpi genes: Rpi-amr1e and the Rpi-amr1e orthologs (U.S. Provisional Pat. App. No. 62/435,451; filed Dec. 16, 2016), Rpi-amr3i (Accession No. KT373889; SEQ ID NO: 1 of WO 2016/182881) Rpi-blb1 (also known as “RB”; Accession Nos. FB764493.1 and AY336128.1), Rpi-sto1 (Accession No. EU884421), Rpi-pta1 (Accession No. EU884422), Rpi-blb2 (Accession No. DQ122125), Rpi-blb3 (Accession No. FJ536326), Rpi-abpt (Accession No. FJ536324), R2-like (Accession No. FJ536323), R2 (Accession No. FJ536325), Rpi-edn1.1 (Accession No. GU563963), Rpi-edn1.2, Rpi-snk1.1, Rpi-snk1.2, Rpi-hjt1.1-IRpi-hjt1.3 (Accession No. GU563971-3), Rpi-bt1 (Accession No. FJ188415), R1 (Accession No. AF447489), R3a (Accession No. AY849382), R3b (Accession No. JF900492), Rpi-vnt1.1 (Accession No. FJ423044), Rpi-vnt1.2 (Accession No. FJ423045), Rpi-vnt1.3 (Accession No. FJ423046), Rpi-mcq1 (Accession No. GN043561), Rpi-chc, Ph-3 (Accession No. KJ563933), and R8 (Accession No. KU530153). The nucleotide sequences corresponding to the accession numbers of either the genes listed above or any genes or proteins disclosed elsewhere herein can be obtained from publicly accessible, online nucleotide and amino acid sequence databases such as, for example, the GenBank and EMBL databases (available on the World Wide Web at ncbi.nlm.nih.gov/genbank and ebi.ac.uk, respectively).

A plant of the invention comprising multiple R genes can be produced, for example, by transforming a plant that already comprises one or more other R gene nucleotide sequences with a heterologous polynucleotide comprising an R gene nucleotide sequence of the present invention including, for example, an c630 or c516 nucleotide sequence. Such a plant that already comprises one or more other R gene nucleotide sequences can comprise R genes that are native to the genome or the plant, that were introduced into the plant via sexual reproduction, or that were introduced by transforming the plant or a progenitor thereof with an R gene nucleotide sequence. Alternatively, the one or more other R gene nucleotide sequences can be introduced into a plant of the invention, which already comprises a heterologous polynucleotide of the invention, by, for example, transformation or sexual reproduction.

In other embodiments, two or more different R gene sequences can be introduced into a plant by stably transforming the plant with a heterologous polynucleotide or vector comprising two or more R gene nucleotide sequences. It is recognized that such an approach can be preferred for plant breeding as it is expected that the two or more R gene nucleotide sequences will be tightly linked and thus, segregate a single locus. Alternatively, a heterologous polynucleotide of the present invention can be incorporated into the genome of a plant in the immediate vicinity of another R gene nucleotide sequence using homologous recombination-based genome modification methods that are described elsewhere herein or otherwise known in the art.

The present invention further provides methods for enhancing the resistance of a plant to a plant disease caused by at least one potyvirus, particularly at least one strain of PVY and/or at least one strain of PVA. The methods comprise modifying at least one plant cell to comprise a heterologous polynucleotide, and optionally regenerating a plant from the modified plant comprising the heterologous polynucleotide. In a first aspect, the methods for enhancing the resistance of a plant to a plant disease caused by at least one potyvirus comprise introducing a heterologous polynucleotide of the invention into at least one plant cell, particularly a plant cell from a solanaceous plant. In certain embodiments, the heterologous polynucleotide is stably incorporated into the genome of the plant cell.

In a second aspect, the methods for enhancing the resistance of a plant to a plant disease caused by at least one potyvirus, particularly at least one strain of PVY and/or at least one strain of PVA, involve the use of a genome-editing method to modify the nucleotide sequences of a native or non-native gene in the genome of the plant cell to comprise a heterologous polynucleotide of the present invention. The methods comprise introducing a nucleic acid molecule into the plant cell, wherein the nucleic acid molecule comprises a nucleotide sequence comprising at least a part of the R gene nucleotide sequence of the present invention and wherein at least a part of the nucleotide sequence of the native or non-native gene is replaced with at least a part of the nucleotide sequence of the nucleic acid molecule. Thus, the methods of the invention involve gene replacement to produce a heterologous polynucleotide of the present invention in the genome of a plant cell.

If desired, the methods of the first and/or second aspect(s) can further comprise regenerating the plant cell into a plant comprising in its genome the heterologous polynucleotide. Preferably, such a regenerated plant comprises enhanced resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA, relative to the resistance of a control plant to the plant disease or diseases caused by the same potyvirus(es), strain(s) of PVY and/or strain(s) of PVA.

The methods of the present invention for enhancing the resistance of a plant to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA can further comprise producing a plant comprising two, three, or more nucleotide sequences encoding an R protein, preferably each nucleotide sequence encoding a different R protein. Such a plant comprising multiple R gene nucleotide sequences comprises one or more additional R gene nucleotide sequences of the present invention and/or any other nucleotide sequence encoding an R protein known in the art. It is recognized that the methods of the first and/or second aspect can be used to produce such a plant comprising multiple nucleotide sequences encoding an R protein. Moreover, it is recognized that a heterologous polynucleotide of the present invention can comprise, for example, one or more R gene nucleotide sequences of the present invention or at least one R gene nucleotide sequences of the present invention and one or more nucleotide sequences encoding an R protein that is known in the art.

The plants disclosed herein find use in methods for limiting plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA in agricultural crop production, particularly in regions where such a plant disease is prevalent and is known to negatively impact, or at least has the potential to negatively impact, agricultural yield. The methods of the invention comprise planting a plant (e.g. a seedling), tuber, or seed of the present invention, wherein the plant, tuber, or seed comprises at least one R gene nucleotide sequence of the present invention. The methods further comprise growing the plant that is derived from the seedling, tuber, or seed under conditions favorable for the growth and development of the plant, and optionally harvesting at least one fruit, tuber, leaf, or seed from the plant.

The present invention additionally provides methods for identifying a solanaceous plant that comprises an R gene for a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA. The methods find use in breeding solanaceous plants for resistance to plant diseases caused PVY, PVA, and/or other potyviruses. Such resistant plants find use in the agricultural production of fruits, tubers, leaves, and/or seeds for human or livestock consumption or other use. The methods comprise detecting in a solanaceous plant, or in at least one part or cell thereof, the presence of: a c630 nucleotide sequence of the present invention, a c516 nucleotide sequence of the present invention, or both a c630 nucleotide sequence and a c516 nucleotide sequence. In some embodiments of the invention, detecting the presence of the c630 or c516 nucleotide sequence comprises detecting the entire c630 or c516 nucleotide sequence in genomic DNA isolated from a solanaceous plant. In preferred embodiments, however, detecting the presence of a c630 or c516 nucleotide sequence comprises detecting the presence of at least one marker within the c630 or c516 nucleotide sequence, respectively. In other embodiments of the invention, detecting the presence of a c630 nucleotide sequence comprises detecting the presence of either one, or both, of the R proteins encoded by the c630 nucleotide sequence using, for example, immunological detection methods involving an antibody preparation specific to C630-SV1 and/or an antibody preparation specific to C630-SV2. Alternatively, an antibody preparation (e.g. polyclonal antibody) that is capable of binding to both C630-SV1 and C630-SV2 can be used if the separate detection of the variant C630 proteins is not desired. In yet embodiments of the invention, detecting the presence of a nucleotide sequence comprises detecting the presence of the R protein encoded by the c516 nucleotide sequence using, for example, immunological detection methods involving antibodies specific to C516.

In the methods for identifying a solanaceous plant that comprises an R gene for a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA, detecting the presence of the c630 nucleotide sequence and/or the c516 nucleotide sequence in the solanaceous plant can involve one or more of the following molecular biology techniques that are disclosed elsewhere herein or otherwise known in the art including, but not limited to, isolating genomic DNA and/or RNA from the plant, amplifying nucleic acid molecules comprising the c630 nucleotide sequence and/or the c516 nucleotide sequence and/or marker(s) therein by PCR amplification, sequencing nucleic acid molecules comprising the c630 nucleotide sequence and/or the c516 nucleotide sequence and/or marker(s), identifying the c630 nucleotide sequence and/or the c516 nucleotide sequence, the marker(s), or a transcript or transcripts of the c630 nucleotide sequence and/or a transcript the c516 nucleotide sequence by nucleic acid hybridization, and conducting an immunological assay for the detection of the R protein(s) encoded by the c630 nucleotide sequence and/or the c516 nucleotide sequence. It is recognized that oligonucleotide probes and PCR primers can be designed to identity the c630 nucleotide sequence and/or the c516 nucleotide sequence of the present invention and that such probes and PCR primers can be utilized in methods disclosed elsewhere herein or otherwise known in the art to rapidly identify in a population of plants one or more plants comprising the presence of an c630 nucleotide sequence and/or an c516 nucleotide sequence of the present invention.

Depending on the desired outcome, the heterologous polynucleotides of the invention can be stably incorporated into the genome of the plant cell or not stably incorporated into genome of the plant cell. If, for example, the desired outcome is to produce a stably transformed plant with enhanced resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA, then the heterologous polynucleotide can be, for example, fused into a plant transformation vector suitable for the stable incorporation of the heterologous polynucleotide into the genome of the plant cell. Typically, the stably transformed plant cell will be regenerated into a transformed plant that comprises in its genome the heterologous polynucleotide. Such a stably transformed plant is capable of transmitting the heterologous polynucleotide to progeny plants in subsequent generations via sexual and/or asexual reproduction. Plant transformation vectors, methods for stably transforming plants with an introduced heterologous polynucleotide and methods for plant regeneration from transformed plant cells and tissues are generally known in the art for both monocotyledonous and dicotyledonous plants or described elsewhere herein.

In other embodiments of the invention in which it is not desired to stably incorporate the heterologous polynucleotide in the genome of the plant, transient transformation methods can be utilized to introduce the heterologous polynucleotide into one or more plant cells of a plant. Such transient transformation methods include, for example, viral-based methods which involve the use of viral particles or at least viral nucleic acids. Generally, such viral-based methods involve constructing a modified viral nucleic acid comprising a heterologous polynucleotide of the invention operably linked to the viral nucleic acid and then contacting the plant either with a modified virus comprising the modified viral nucleic acid or with the viral nucleic acid or with the modified viral nucleic acid itself. The modified virus and/or modified viral nucleic acids can be applied to the plant or part thereof, for example, in accordance with conventional methods used in agriculture, for example, by spraying, irrigation, dusting, or the like. The modified virus and/or modified viral nucleic acids can be applied in the form of directly sprayable solutions, powders, suspensions or dispersions, emulsions, oil dispersions, pastes, dustable products, materials for spreading, or granules, by means of spraying, atomizing, dusting, spreading or pouring. It is recognized that it may be desirable to prepare formulations comprising the modified virus and/or modified viral nucleic acids before applying to the plant or part or parts thereof. Methods for making pesticidal formulations are generally known in the art or described elsewhere herein.

The present invention provides nucleic acid molecules comprising c630 nucleotide sequences and nucleic acid molecules comprising c516 nucleotide sequences. Preferably, such nucleic acid molecules are capable of conferring upon a host plant, particularly a solanaceous host plant, enhanced resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA. Thus, such nucleic acid molecules find use in limiting a plant disease caused by PVY, PVA, and/or other potyviruses in agricultural production. The nucleic acid molecules of the present invention include, but are not limited to, nucleic acid molecules comprising at least one of the c630 and c516 nucleotide sequence disclosed herein but also additional orthologs and other variants of the c630 and c516 nucleotide sequences that are capable of conferring to a plant resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA. Methods are known in the art or otherwise disclosed herein for determining resistance of a plant a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA, including, for example, the assays described hereinbelow.

Additionally provided are methods for introducing c630 and/or c516 into a solanaceous plant lacking in its genome c630 (SEQ ID NO: 1, 10, or 13) and/or c516 (SEQ ID NO: 6 or 12). The methods comprise crossing (i.e. cross-pollinating) a first solanaceous plant comprising in its genome at least one copy of c630 and/or c516 with a second solanaceous plant lacking in its genome c630 and/or c516. The first and second solanaceous plants can be the same solanaceous species or can be different solanaceous species. For example, the first solanaceous plant can be a S. stoloniferum plant or S. tuberosum plant and the second solanaceous plant can be S. tuberosum lacking c630 and/or c516. Such a crossing of a first species of a plant to a second species of a plant is known as an interspecific hybridization and can be used to introgress a gene or genes of interest (e.g. c630) from one species into a related species lacking the gene or genes of interest and typically involves multiple generations of backcrossing of the progeny with the related species and selection at each generation of progeny comprising the gene or genes of interest. Such interspecific hybridization, introgression, and backcrossing methods are well known in the art and can be used in the methods of the present invention. See “Principals of Cultivar Development,” Fehr, 1993, Macmillan Publishing Company, New York; and “Fundamentals of Plant Genetics and Breeding,” Welsh, 1981, John Wiley & Sons, Inc., New York.

In methods of the present invention for introducing c630 and/or c516 into a solanaceous plant lacking in its genome c630 and/or c516, either the first solanaceous plant or the second solanaceous plant can be the pollen donor plant. For example, if the first solanaceous plant is the pollen donor plant, then the second solanaceous plant is the pollen-recipient plant. Likewise, if the second solanaceous plant is the pollen donor plant, then the first solanaceous plant is the pollen-recipient plant. Following the crossing, the pollen-recipient plant is grown under conditions favorable for the growth and development of the plant and for a sufficient period of time for seed to mature or to achieve an otherwise desirable growth stage for use in a subsequent in vitro germination procedure such as, for example, embryo rescue that is described below. The seed can then be harvested and those seed comprising c630 and/or c516 identified by any method known in the art including, for example, the methods for identifying a solanaceous plant that comprises an R gene for a plant disease caused by at least one strain of PVY and at least one strain of PVA that are described elsewhere herein. In certain embodiments, the first solanaceous plant is a S. stoloniferum or a S. tuberosum plant comprising c630 and/or c516 and the second plant is S. tuberosum plant lacking c630 and/or c516.

It is recognized, however, that in certain embodiments of the invention involving interspecific hybridizations, it may be advantageous to harvest the seed resulting from such interspecific hybridizations at an immature growth stage and then to germinate the immature seeds in culture (i.e. in vitro), whereby the seeds are allowed germinate in culture using methods known in art as “embryo rescue” methods. See Reed (2005) “Embryo Rescue,” in Plant Development and Biotechnology, Trigiano and Gray, eds. CRC Press, Boca Raton, pp. 235-239; and Sharma et al. (1996) Euphytica 89: 325-337. It is further recognized that “embryo rescue methods are typically used when mature seeds produced by an interspecific cross display little or no germination, whereby few or no interspecific hybrid plants are produced.

The methods of the present invention find use in producing plants with enhanced resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA. Typically, the methods of the present invention will enhance or increase the resistance of the subject plant to the plant disease by at least 25%, 50%, 75%, 100%, 150%, 200%, 250%, 500% or more when compared to the resistance of a control plant to the same potyvirus(es), strain(s) of PVY and/or strain(s) of PVA. Unless stated otherwise or apparent from the context of a use, a control plant for the present invention is a plant that does not comprise the heterologous polynucleotide, the c630 nucleotide sequence and/or the c516 nucleotide sequence of the present invention. Preferably, the control plant is essentially identical (e.g. same species, subspecies, and variety) to the plant comprising the heterologous polynucleotide of the present invention except the control does not comprise the heterologous polynucleotide, the c630 nucleotide sequence and/or the c516 nucleotide sequence. In some embodiments, the control will comprise a heterologous, control polynucleotide (e.g. vector control) that does comprise the one or more c630 and/or c516 nucleotide sequences that are in a heterologous polynucleotide of the present invention.

Additionally, the present invention provides transformed plants, seeds, and plant cells produced by the methods of present invention and/or comprising a heterologous polynucleotide of the present invention. Also provided are progeny plants and seeds thereof comprising a heterologous polynucleotide of the present invention. The present invention also provides fruits, seeds, tubers, leaves, stems, roots, and other plant parts produced by the transformed plants and/or progeny plants of the invention as well as food products and other agricultural products comprising, or produced or derived from, the plants or any part or parts thereof including, but not limited to, fruits, tubers, leaves, stems, roots, and seed. Other agricultural products include, for example, smoking products produced from tobacco leaves (e.g., cigarettes, cigars, and pipe and chewing tobacco) and food and industrial starch products produced from potato tubers. It is recognized that such food products can be consumed or used by humans and other animals including, but not limited to, pets (e.g., dogs and cats), livestock (e.g., pigs, cows, chickens, turkeys, and ducks), and animals produced in freshwater and marine aquaculture systems (e.g. fish, shrimp, prawns, crayfish, and lobsters).

Non-limiting examples of the compositions and methods of the present invention are as follows:

1. A nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence set forth in SEQ ID NO: 1, 6, 10, 12, or 13;

(b) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 2, 4, or 7, and optionally, wherein the nucleotide sequence is not naturally occurring;

(c) the nucleotide sequence set forth in SEQ ID NO: 3, 5, 8, 9, or 11;

(d) a nucleotide sequence having at least 90% sequence identity to at least one of the nucleotide sequences set forth in SEQ ID NOS: 1, 3, 5, 6, 8, 10, 12, and 13, wherein the nucleic acid molecule is capable of conferring resistance to a plant disease caused by at least one strain of Potato virus Y (PVY), at least one strain of Potato virus A (PVA), and/or at least one potyvirus, relative to a control plant not comprising the nucleic acid molecule and optionally, wherein the nucleotide sequence is not naturally occurring; and

(e) a nucleic acid molecule comprising a nucleotide sequence encoding an amino acid sequence having at least 90% sequence identity to at least one of the amino acid sequences set forth in SEQ ID NO: 2, 4 and 7, wherein the nucleic acid molecule is capable of conferring resistance to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, relative to a control plant not comprising the nucleic acid molecule and optionally, wherein the nucleotide sequence is not naturally occurring.

2. The nucleic acid molecule of embodiment 1, wherein the nucleic acid molecule is an isolated nucleic acid molecule. 3. An expression cassette comprising the nucleic acid molecule of embodiment 1 or 2 and an operably linked heterologous promoter. 4. A vector comprising the nucleic acid molecule of embodiment 1 or 2 or the expression cassette of embodiment 3. 5. A vector of embodiment 4, further comprising an additional R gene. 6. A host cell transformed with the nucleic acid molecule of embodiment 1 or 2, the expression cassette of embodiment 3, or the vector of embodiment 4 or 5. 7. The host cell of embodiment 6, wherein the host cell is a plant cell, a bacterium, a fungal cell, or an animal cell. 8. The host cell of embodiment 6 or 7, wherein the host cell is a solanaceous plant cell. 9. A plant or plant cell comprising the nucleic acid molecule of embodiment 1 or 2, the expression cassette of embodiment 3, or the vector of embodiment 4 or 5. 10. The plant or plant cell of embodiment 9, wherein the plant is a solanaceous plant and the plant cell is a solanaceous plant cell. 11. The plant of embodiment 10, wherein the solanaceous plant is the solanaceous plant is selected from the group consisting of potato, tomato, eggplant, pepper, tomatillo, tobacco, and petunia. 12. A plant or plant cell comprising stably incorporated in its genome a heterologous polynucleotide comprising a nucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence set forth in SEQ ID NO: 1, 6, 10, 12, or 13;

(b) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 2, 4, or 7;

(c) the nucleotide sequence set forth in SEQ ID NO: 3, 5, 8, 9, or 11;

(d) a nucleotide sequence having at least 90% sequence identity to at least one of the nucleotide sequences set forth in SEQ ID NOS: 1, 3, 5, 6, 8, 10, 12, and 13, wherein the nucleic acid molecule is capable of conferring resistance to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, relative to a control plant not comprising the nucleic acid molecule; and

(e) a nucleic acid molecule comprising a nucleotide sequence encoding an amino acid sequence having at least 90% sequence identity to at least one of the amino acid sequences set forth in SEQ ID NO: 2, 4 and 7, wherein the nucleic acid molecule is capable of conferring resistance to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, relative to a control plant not comprising the nucleic acid molecule.

13. The plant or plant cell of embodiment 12, wherein the heterologous polynucleotide comprises the nucleotide sequence of any one of (b)-(e) and further comprises a promoter operably linked for the expression of the nucleotide sequence in a plant. 14. The plant or plant cell of embodiment 13, wherein the promoter is selected from the group consisting of pathogen-inducible, constitutive, tissue-preferred, wound-inducible, and chemical-regulated promoters. 15. The plant or plant cell of any one of embodiments 12-14, wherein the plant or plant cells is a solanaceous plant or plant cell. 16. The plant or plant cell of any one of embodiments 12-15, wherein the solanaceous plant or plant cell is selected from the group consisting of potato, tomato, eggplant, pepper, tomatillo, tobacco, and petunia. 17. The plant or plant cell of any one of embodiments 12-16, wherein the plant or plant cell comprises enhanced resistance to a plant disease caused by at least one strain of PVY and/or PVA, relative to the resistance of a control plant. 18. The plant or plant cell of embodiment 17, wherein the plant or plant cell comprises enhanced resistance to plant disease(s) caused by at least two strains of PVY and/or PVA, relative to a control plant. 19. The plant or plant cell of any one of embodiments 12-18, wherein the plant or plant cell is a potato or tomato plant or plant cell. 20. A method for enhancing the resistance of a plant to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, the method comprising modifying at least one plant cell to comprise a heterologous polynucleotide, the heterologous polynucleotide comprising a nucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence set forth in SEQ ID NO: 1, 6, 10, 12, or 13;

(b) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 2, 4, or 7;

(c) the nucleotide sequence set forth in SEQ ID NO: 3, 5, 8, 9, or 11;

(d) a nucleotide sequence having at least 90% sequence identity to at least one of the nucleotide sequences set forth in SEQ ID NOS: 1, 3, 5, 6, 8, 10, 12, and 13, wherein the nucleic acid molecule is capable of conferring resistance to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, relative to a control plant not comprising the nucleic acid molecule; and

(e) a nucleic acid molecule comprising a nucleotide sequence encoding an amino acid sequence having at least 90% sequence identity to at least one of the amino acid sequences set forth in SEQ ID NO: 2, 4 and 7, wherein the nucleic acid molecule is capable of conferring resistance to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, relative to a control plant not comprising the nucleic acid molecule.

21. The method of embodiment 20, wherein the heterologous polynucleotide is stably incorporated into the genome of the plant cell. 22. The method of embodiment 20 or 21, wherein the plant cell is regenerated into a plant comprising in its genome the heterologous polynucleotide. 23. The method of any one of embodiments 20-22, wherein modifying at least one plant cell to comprise a heterologous polynucleotide comprises introducing the heterologous polynucleotide into at least one plant cell. 24. The method of any one of embodiments 20-23, wherein the heterologous polynucleotide comprises the nucleotide sequence of any one of (b)-(e) and further comprises a promoter operably linked for the expression of the nucleotide sequence in a plant. 25. The method of embodiment 24, wherein the promoter is selected from the group consisting of pathogen-inducible, constitutive, tissue-preferred, wound-inducible, and chemical-regulated promoters. 26. The method of any one of embodiments 20-22, wherein modifying at least one plant cell to comprise a heterologous polynucleotide comprises using genome editing to modify the nucleotide sequences of a native or non-native gene in the genome of the plant cell to comprise the nucleotide sequence of any one of (a)-(e). 27. The method of embodiment 26, wherein the modifying further comprise introducing a nucleic acid molecule into the plant cell, wherein the nucleic acid molecule comprises a nucleotide sequence comprising at least a part of the nucleotide sequence of any one of (a)-(e). 28. The method of embodiment 27, wherein at least a portion of the at least a part of the nucleotide sequence of the native or non-native gene is replaced with at least a part of the nucleotide sequence of the nucleic acid molecule. 29. The method of any one of embodiments 20-28, wherein the plant comprising the heterologous polynucleotide comprises enhanced resistance to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, relative to the resistance of a control plant. 30. The method of any one of embodiments 20-29, wherein the plant comprising the heterologous polynucleotide comprises enhanced resistance to plant disease(s) caused by at least two strains of PVY and/or PVA, relative to the resistance of a control plant. 31. The method of any one of embodiments 20-30, wherein the plant is selected from the group consisting of potato, tomato, eggplant, pepper, tomatillo, tobacco, and petunia. 32. A plant produced or producible by the method of any one of embodiments 20-31. 33. A fruit, tuber, leaf, or seed of the plant of any one of embodiments 9-19 and 32, wherein the fruit, tuber, leaf or seed comprises the heterologous polynucleotide. 34. A method of limiting a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus in agricultural crop production, the method comprising planting a seedling, tuber, or seed of the plant of any one of embodiments 9-19 and 32 and growing the seedling, tuber, or seed under conditions favorable for the growth and development of a plant resulting therefrom, wherein the seedling, tuber, or seed comprises the nucleic acid molecule, expression cassette, vector, or heterologous polynucleotide. 35. The method of embodiment 34, further comprising harvesting at least one fruit, tuber, leaf and/or seed from the plant, and optionally processing the harvested fruit, tuber, leaf, and/or seed into a food product. 36. A fruit, tuber, leaf, seed, or food product obtained or obtainable using the method of claim 35. 37. A method for identifying a solanaceous plant that comprises an R gene for a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, the method comprising detecting in the plant, or in at least one part or cell thereof, the presence of: a c630 nucleotide sequence, a c516 nucleotide sequence, or a c630 nucleotide sequence and a c516 nucleotide sequence. 38. The method of embodiment 37, wherein the solanaceous plant comprises enhanced resistance to at plant disease(s) caused by at least two strains of PVY and/or PVA. 39. The method of embodiment 37 or 38, wherein the solanaceous plant is a potato or tomato plant. 40. The method of any one of embodiments 37-39, wherein the presence of the c630 nucleotide sequence is detected by detecting at least one marker within the c630 nucleotide sequence and wherein the presence of the c516 nucleotide sequence is detected by detecting at least one marker within the c516 nucleotide sequence. 41. The method of any one of embodiments 37-40, wherein the c630 nucleotide sequence comprises or consists of the nucleotide sequence set forth in SEQ ID NOS: 1, 3, 5, 10, or 12 and wherein the c516 nucleotide sequence comprises or consists of the nucleotide sequence set forth in SEQ ID NOS: 6, 8, or 12. 42. The method of any one of embodiments 37-41, wherein detecting the presence of the c630 and/or c516 nucleotide sequence comprises a member selected from the group consisting of PCR amplification, nucleic acid sequencing, nucleic acid hybridization, and an immunological assay for the detection of (i) either one or both of the R proteins encoded by the c630 nucleotide sequence and/or (ii) the R protein encoded by the c516 nucleotide sequence. 43. A solanaceous plant identified or indentifiable by the method of any one of embodiments 37-42. 44. The solanaceous plant of embodiment 43, wherein the solanaceous plant is selected from the group consisting of potato, tomato, eggplant, pepper, tomatillo, tobacco, and petunia. 45. A fruit, tuber, leaf, or seed of the solanaceous plant of embodiment 43 or 44. 46. A solanaceous plant or plant cell comprising c630 or c516, wherein the plant is not a Solanum stoloniferum plant or a Solanum tuberosum plant. 47. The solanaceous plant of embodiment 46, wherein the solanaceous plant comprises enhanced resistance to at least one strain of PVY and/or PVA. 48. A method for introducing c630 and/or c516 into a solanaceous plant, the method comprising:

(a) crossing a first solanaceous plant comprising in its genome at least one copy of c630, c516, or both c630 and c516, with a second solanaceous plant lacking in its genome c630, c516, or both c630 and c516, respectively, whereby at least one progeny plant is produced; and

(b) selecting at least one progeny plant comprising in its genome c630, c516, or both c630 and c516 by detecting in the progeny plant the presence of c630, c516, or both c630 and c516, respectively.

49. The method of embodiment 48, wherein the first solanaceous plant is a S. stoloniferum plant or a S. tuberosum plant and the second solanaceous plant is S. tuberosum plant lacking in its genome c630 and/or c516. 50. The method of embodiment 48 or 49, wherein c630 comprises or consists of a nucleotide sequence selected from the group consisting of the nucleotide sequences set forth in SEQ ID NOS: 1, 10, and 13. 51. The method of any one of embodiments 48-50, wherein c516 comprises or consists of a nucleotide sequence selected from the group consisting of the nucleotide sequences set forth in SEQ ID NOS: 6 and 12. 52. The method of any one of embodiments 48-51, wherein detecting in the progeny plant the presence of c630, c516, or both c630 and c516 comprises detecting in the progeny plant, or in at least one part or cell thereof, the presence of a c630 nucleotide sequence, a c516 nucleotide sequence, or a c630 nucleotide sequence and a c516 nucleotide sequence, respectively, using the method according to any one of embodiments 37-42. 53. The method of any one of embodiments 48-52, further comprising (i) backcrossing at least one selected progeny plant of (b) to a solanaceous plant that is of the same species and genotype as second solanaceous plant or of the same species as the second solanaceous plant and lacking in its genome c630, c516, or both c630 and c516, whereby at least one progeny plant is produced from the backcrossing; and (ii) selecting at least one progeny plant comprising in its genome c630, c516, or both c630 and c516 that is produced from the backcrossing of (i). 54. A progeny plant obtained or obtainable using the method of any one of embodiments 48-53. 55. The progeny plant of embodiment 54, wherein the progeny plant comprises enhanced resistance to at least one strain of PVY and/or PVA. 56. A fruit, tuber, leaf, or seed obtained or obtainable from the solanaceous plant of embodiment 54 or 55. 57. Use of the plant, fruit, tuber, leaf or seed of any one of embodiments 9-19, 32, 33, 43-47, and 54-56 in agriculture. 58. A human or animal food product comprising, or produced using, the plant, fruit, tuber, leaf, and/or seed of any one of embodiments 9-19, 32, 33, 43-47, and 54-56. 59. A polypeptide comprising an amino acid sequence selected from the group consisting of:

(a) the amino acid sequence encoded by the nucleotide sequence set forth in SEQ ID NO: 2, 4, or 7;

(b) the amino acid sequence encoded by the nucleotide sequence set forth in SEQ ID NO: 1, 3, 5, 6, 8, 9, 10, 11, 12, or 13; and

(c) an amino acid sequence having at least 90% sequence identity to at least one of the amino acid sequences set forth in SEQ ID NO: 2, 4, and 7, wherein a polypeptide comprising the amino acid sequence is capable of conferring resistance to a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, relative to a control plant not comprising the polypeptide the polypeptide.

Additional embodiments of the methods and compositions of the present invention are described elsewhere herein.

Preferred plants of the invention are solanaceous plants. As used herein, the term “solanaceous plant” refers to a plant that is a member of the Solanaceae family. Such solanaceous plants include, for example, domesticated and non-domesticated members of Solanaceae family. Solanaceous plants of the present invention include, but are not limited to, potato (Solanum tuberosum), eggplant (Solanum melongena), petunia (Petunia spp., e.g., Petunia x hybrida or Petunia hybrida), tomatillo (Physalis philadelphica), other Physalis spp., woody nightshade (Solanum dulcamara), garden huckleberry (Solanum scabrum), gboma eggplant (Solanum macrocarpon), pepper (Capsicum spp; e.g., Capsicum annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, and the like), tomato (Solanum lycopersicum or Lycopersicon esculentum), tobacco (Nicotiana spp., e.g. N. tabacum, N. benthamiana), Solanum americanum, Solanum demissum, Solanum stoloniferum, Solanum papita, Solanum bulbocastanum, Solanum edinense, Solanum schenckii, Solanum hjertingii, Solanum venturi, Solanum mochiquense, Solanum chacoense, and Solanum pimpinellifolium. In preferred embodiments of the methods and compositions of the present invention, the solanaceous plants are solanaceous plants grown in agriculture including, but not limited to, potato, tomato, eggplant, pepper, tomatillo, tobacco and petunia. In more preferred embodiments, the solanaceous plants are potato and tomato. In even more preferred embodiments, the preferred plant is potato.

Other plants of interest for the methods and compositions of the present invention include, for example, any plant that is a host for PVY, PVA, and/or other Potyvirus. Such plants include, but are not limited to, plant species in the following plant families: Amaranthaceae (particularly in the subfamily Chenopodiaceae), Leguminosae, and Compositae.

Examples of other plant species of interest for the compositions and methods of the present invention include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), triticale (x Triticosecale or Triticum x Secale) sorghum (Sorghum bicolor, Sorghum vulgare), teff (Eragrostis tef), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), switchgrass (Panicum virgatum), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), strawberry (e.g. Fragaria x ananassa, Fragaria vesca, Fragaria moschata, Fragaria virginiana, Fragaria chiloensis), sweet potato (Ipomoea batatus), yam (Dioscorea spp., D. rotundata, D. cayenensis, D. alata, D. polystachya, D. bulbifera, D. esculenta, D. dumetorum, D. trifda), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), oil palm (e.g. Elaeis guineensis, Elaeis oleifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), date (Phoenix dactyhfera), cultivated forms of Beta vulgaris (sugar beets, garden beets, chard or spinach beet, mangelwurzel or fodder beet), spinach (Spinacia oleracea), sugarcane (Saccharum spp.), quinoa (Chenopodium quinoa), oat (Avena sativa), barley (Hordeum vulgare), cannabis (Cannabis sativa, C. indica, C. ruderalis), poplar (Populus spp.), eucalyptus (Eucalyptus spp.), Arabidopsis thaliana, Arabidopsis rhizogenes, Nicotiana benthamiana, Brachypodium distachyon vegetables, ornamentals, and conifers and other trees. In specific embodiments, plants of the present invention are crop plants (e.g. maize, sorghum, wheat, millet, rice, barley, oats, sugarcane, alfalfa, soybean, peanut, sunflower, cotton, safflower, Brassica spp., lettuce, strawberry, apple, citrus, etc.).

Vegetables include tomatoes (Lycopersicon esculentum), eggplant (also known as “aubergine” or “brinjal”) (Solanum melongena), pepper (Capsicum annuum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), chickpeas (Cicer arietinum), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum. Fruit trees and related plants include, for example, apples, pears, peaches, plums, oranges, grapefruits, limes, pomelos, palms, and bananas. Nut trees and related plants include, for example, almonds, cashews, walnuts, pistachios, macadamia nuts, filberts, hazelnuts, and pecans.

The term “solanaceous plant” is intended to encompass solanaceous plants at any stage of maturity or development, as well as any cells, tissues or organs (plant parts) taken or derived from any such plant unless otherwise clearly indicated by context. Solanaceous plant parts include, but are not limited to, fruits, stems, tubers, roots, flowers, ovules, stamens, leaves, embryos, meristematic regions, callus tissue, anther cultures, gametophytes, sporophytes, pollen, microspores, protoplasts, and the like. As used herein, the term “tuber” is intended to mean a whole tuber or any part thereof such as, for example, a slice or a portion of potato tuber comprising one or more buds (i.e. “eyes”) suitable for planting in a field to produce a potato plant. The present invention also includes seeds produced by the solanaceous plants of the present invention.

The present invention provides resistance nucleic acid molecules that are capable of conferring to a plant resistance to a plant disease caused by at least one plant pathogen, plants and plants cells comprising such nucleic acid molecules and related methods. Plant pathogens include, for example, viruses, bacteria, fungi, oomycetes, nematodes, and the like. Preferred plant pathogens of the present invention are viruses, particularly viruses in the family Potyviridae, more particularly viruses in the genus Potyvirus, most particularly PVY and PVA. Virus species of interest in the in the family Potyviridae include, but are not limited to, virus species in the following genera: Potyvirus, Ipomovirus, Brambyvirus, Tritimovirus, Rymovirus, Bymovirus, Poacevirus, and Macluravirus. Examples of Potyvirus species of interest for the compositions and methods of the present invention include, but are not limited to, Alstroemeria mosaic potyvirus, Amaranthus leaf mottle potyvirus, Apium virus Y, Araujia mosaic potyvirus, Arracacha Y potyvirus, Artichoke latent potyvirus, Asparagus 1 potyvirus, Banana bract mosaic potyvirus, Bean common mosaic necrosis potyvirus, Bean common mosaic potyvirus, Bean yellow mosaic potyvirus, Beet mosaic potyvirus, Bidens mosaic potyvirus, Bidens mottle virus, Brugmansia mosaic virus, Caladenia virus A, Canna yellow streak virus, Cardamom mosaic potyvirus, Carnation vein mottle potyvirus, Carrot thin leaf potyvirus, Cassava brown streak potyvirus, Cassia yellow spot potyvirus, Celery mosaic virus, Chickpea bushy dwarf potyvirus, Chickpea distortion mosaic potyvirus, Chilli ringspot virus[2], Chilli veinal mottle virus, Clitoria chlorosis virus, Clover yellow vein virus, Cocksfoot streak virus, Commelina diffusa potyvirus, Commelina mosaic virus, Cowpea green vein-banding potyvirus, Cowpea Moroccan aphid-borne mosaic potyvirus, Cowpea rugose mosaic potyvirus, Crinum mosaic potyvirus, Daphne Y potyvirus, Dasheen mosaic potyvirus, Datura Colombian potyvirus, Datura distortion mosaic potyvirus, Datura necrosis potyvirus, Datura shoestring potyvirus, Dendrobium mosaic potyvirus, Desmodium mosaic potyvirus, Dioscorea alata potyvirus, Dioscorea green banding mosaic potyvirus, Eggplant green mosaic potyvirus, Euphorbia ringspot potyvirus, Freesia mosaic potyvirus, Groundnut eyespot potyvirus, Guar symptomless potyvirus, Guinea grass mosaic potyvirus, Hardenbergia mosaic virus, Helenium Ypotyvirus, Henbane mosaic potyvirus, Hippeastrum mosaic potyvirus, Hyacinth mosaic potyvirus, Iris fulva mosaic potyvirus, Iris mild mosaic potyvirus, Iris severe mosaic potyvirus, Japanese hornwort mosaic virus, Johnsongrass mosaic virus, Kennedya Y potyvirus, Leek yellow stripe potyvirus, Lettuce mosaic potyvirus, Lily mottle potyvirus, Lupine potyvirus, Maize dwarf mosaic potyvirus, Malva vein clearing potyvirus, Marigold mottle potyvirus, Narcissus degeneration virus, Narcissus late season yellows virus, Narcissus yellow stripe virus, Nerine potyvirus, Onion yellow dwarf potyvirus, Ornithogalum mosaic potyvirus, Papaya ringspot potyvirus, Parsnip mosaic potyvirus, Passiflora ringspot potyvirus, Passiflora South African potyvirus, Passiflora virus Y, Passionfruit woodiness virus, Patchouli mosaic potyvirus, Pea mosaic potyvirus, Pea seed-borne mosaic potyvirus, Peanut green mosaic potyvirus, Peanut mottle virus, Pepper Indian mottle potyvirus, Pepper mottle virus, Pepper severe mosaic potyvirus, Pepper vein banding virus, Pepper veinal mottle potyvirus, Plum pox potyvirus, Pokeweed mosaic potyvirus, Potato virus A potyvirus, Potato virus V potyvirus, Potato virus Y, Primula mosaic potyvirus, Ranunculus mottle potyvirus, Shallot yellow stripe potyvirus, Sorghum mosaic potyvirus, Soybean mosaic virus, Statice Ypotyvirus, Sugarcane mosaic virus, Sweetpotato feathery mottle potyvirus, Sweet potato G potyvirus, Sweet potato latent virus, Swordbean distortion mosaic potyvirus, Sunflower chlorotic mottle virus, Tamarillo mosaic potyvirus, Telfairia mosaic potyvirus, Tobacco etch virus, Tobacco vein-banding mosaic potyvirus, Tobacco vein mottling potyvirus, Tobacco wilt potyvirus, Tomato Peru potyvirus, Tradescantia mosaic virus, Triteleia mosaic virus, Tropaeolum 1 potyvirus, Tropaeolum 2 potyvirus, Tuberose potyvirus, Tulip band-breaking potyvirus, Tobacco vein banding mosaic virus, Tulip breaking potyvirus, Tulip chlorotic blotch potyvirus, Turnip mosaic potyvirus, Tradescantia mosaic virus, Ullucus mosaic potyvirus, Vallota mosaic potyvirus, Vanilla mosaic potyvirus, Vanilla necrosis potyvirus, Voandzeia distortion mosaic potyvirus, Watermelon mosaic virus, Wild potato mosaic potyvirus, Wisteria vein mosaic potyvirus, Yam mosaic potyvirus, Zucchini yellow fleckpotyvirus, Zucchini yellow mosaic virus, Asystasia gangetica mottle potyvirus, Celery latent potyvirus, Datura mosaic potyvirus, Endive necrotic mosaic potyvirus, Kalanchoe mosaic potyvirus, Konjak mosaic potyvirus, Nasturtium mosaic potyvirus, Patchouli mottle potyvirus, Shallot yellow stripe potyvirus, Sweetpotato vein mosaic potyvirus, and Welsh onion yellow stripe potyvirus.

In preferred embodiments of the present invention, a nucleic acid molecule of an R gene is capable of conferring to a plant resistance to a plant disease caused by at least one potyvirus.

In more preferred embodiments, a nucleic acid molecule of an R gene is capable of conferring to a plant resistance to a plant disease caused by at least one strain of PVY or PVA. In even more preferred embodiments, a nucleic acid molecule of an R gene is capable of conferring to a plant resistance to a plant disease caused by at least one strain of PVY and at least one strain of PVA.

In yet even more preferred embodiments, a nucleic acid molecule of an R gene is capable of conferring to a plant resistance to a plant disease caused by multiple strains of PVY or PVA. In the most preferred embodiments, a nucleic acid molecule of an R gene is capable of conferring to a plant resistance to a plant disease caused by multiple strains of PVY and multiple strains of PVA.

In one embodiment of the invention, the nucleotide sequences encoding R proteins have at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the entire nucleotide sequence set forth in SEQ ID NO: 1 or 6, or to a fragment thereof. Such fragments include, for example, those comprising or consisting of the entire nucleotide sequence set forth in SEQ ID NO: 10, 12, or 13. In another embodiment of the invention, the nucleotide sequences encoding R proteins have at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the entire nucleotide sequence set forth in SEQ ID NO: 3, 5, and/or 8, or to a fragment thereof.

The present invention encompasses isolated or substantially purified polynucleotide (also referred to herein as “nucleic acid molecule”, “nucleic acid” and the like) or protein (also referred to herein as “polypeptide”) compositions. An “isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment. Thus, an isolated or purified polynucleotide or protein is substantially free of other cellular material or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Optimally, an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived. For example, in various embodiments, the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived. A protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein.

When the protein of the invention or biologically active portion thereof is recombinantly produced, optimally culture medium represents less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors or non-protein-of-interest chemicals.

Fragments and variants of the disclosed polynucleotides and proteins encoded thereby are also encompassed by the present invention. By “fragment” is intended a portion of the polynucleotide or a portion of the amino acid sequence and hence protein encoded thereby.

Fragments of polynucleotides comprising coding sequences may encode protein fragments that retain biological activity of the full-length or native protein. Alternatively, fragments of a polynucleotide that are useful as hybridization probes generally do not encode proteins that retain biological activity or do not retain promoter activity. Thus, fragments of a nucleotide sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length polynucleotide of the invention.

In certain embodiments of the invention, the fragments and variants of the disclosed polynucleotides and proteins encoded thereby are those that are capable of conferring to a plant resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA. Preferably, a polynucleotide comprising a fragment of a native R polynucleotide of the present invention is capable of conferring resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA to a plant comprising the polynucleotide. Likewise, a protein or polypeptide comprising a native R protein of the present invention is preferably capable of conferring resistance to a plant disease caused by at least one potyvirus, at least one strain of PVY, and/or at least one strain of PVA to a plant comprising the protein or polypeptide.

Polynucleotides that are fragments of a native R polynucleotide comprise at least 16, 20, 50, 75, 100, 125, 150, 175, 200, 250, 300, 400, 500, 1000, 2000, 3000, 4000, 5000, 6000, 7000, or 8000 contiguous nucleotides, or up to the number of nucleotides present in a full-length R polynucleotide disclosed herein (for example, 8335, 3315, 3774, 8206, 2817, 5065, 6232, and 7488 nucleotides for of SEQ ID NOS: 1, 3, 5, 6, 8, 10, 12, and 13 respectively).

“Variants” is intended to mean substantially similar sequences. For polynucleotides, a variant comprises a polynucleotide having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a “native” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively. For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the R proteins of the invention. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant polynucleotides also include synthetically derived polynucleotides, such as those generated, for example, by using site-directed mutagenesis but which still encode an R protein of the invention. Generally, variants of a particular polynucleotide of the invention will have at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein. In certain embodiments of the invention, variants of a particular polynucleotide of the invention will have at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to at least one nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 6, 8, 10, 12, and 13, and optionally comprise a non-naturally occurring nucleotide sequence that differs from the nucleotide sequence set forth in SEQ ID NO: 1, 3, 5, 6, 8, 10, 12, and/or 13 by at least one nucleotide modification selected from the group consisting of the substitution of at least one nucleotide, the addition of at least one nucleotide, and the deletion of at least one nucleotide. It is understood that the addition of at least one nucleotide can be the addition of one or more nucleotides within a nucleotide sequence of the present invention (e.g. SEQ ID NO: 1, 3, 5, 6, 8, 10, 12, and 13), the addition of one or more nucleotides to the 5′ end of a nucleotide sequence of the present invention, and/or the addition of one or more nucleotides to the 3′ end of a nucleotide sequence of the present invention.

Variants of a particular polynucleotide of the invention (i.e., the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Thus, for example, a polynucleotide that encodes a polypeptide with a given percent sequence identity to at least one polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NOS: 2, 4, and 7, is disclosed. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides of the invention is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity. In certain embodiments of the invention, variants of a particular polypeptide of the invention will have at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth in SEQ ID NO: 2, 4, or 7, and optionally comprises a non-naturally occurring amino acid sequence that differs from at least one amino acid sequence selected from the group consisting of SEQ ID NO: 2, 4, and 7 by at least one amino acid modification selected from the group consisting of the substitution of at least one amino acid, the addition of at least one amino acid, and the deletion of at least one amino acid. It is understood that the addition of at least one amino acid can be the addition of one or more amino acids within an amino acid sequence of the present invention (e.g. SEQ ID NO: 2, 4, or 7), the addition of one or more amino acids to the N-terminal end of an amino acid sequence of the present invention, and/or the addition of one or more amino acids to the C-terminal end of an amino acid sequence of the present invention.

“Variant” protein is intended to mean a protein derived from the native protein by deletion (so-called truncation) of one or more amino acids at the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more internal sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of an R protein will have at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein (e.g. the amino acid sequence set forth in SEQ ID NO: 2, 4, or 7) as determined by sequence alignment programs and parameters described elsewhere herein. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.

The proteins of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. Methods for mutagenesis and polynucleotide alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al. (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be optimal.

Thus, the genes and polynucleotides of the invention include both the naturally occurring sequences as well as mutant and other variant forms. Likewise, the proteins of the invention encompass naturally occurring proteins as well as variations and modified forms thereof. More preferably, such variants confer to a plant or part thereof comprising the variant enhanced resistance a plant disease caused by at least one strain of PVY and/or PVA. In some embodiments, the mutations that will be made in the DNA encoding the variant will not place the sequence out of reading frame. Optimally, the mutations will not create complementary regions that could produce secondary mRNA structure. See, EP Patent Application Publication No. 75,444.

The deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays. That is, the activity can be evaluated by assays that are disclosed herein below.

Variant polynucleotides and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.

The polynucleotides of the invention can be used to isolate corresponding sequences from other organisms, particularly other plants. In this manner, methods such as PCR, hybridization, and the like can be used to identify such sequences based on their sequence homology to the sequences set forth herein. Sequences isolated based on their sequence identity to the entire sequences set forth herein or to variants and fragments thereof are encompassed by the present invention. Such sequences include sequences that are orthologs of the disclosed sequences. “Orthologs” is intended to mean genes derived from a common ancestral gene and which are found in different species as a result of speciation. Genes found in different species are considered orthologs when their nucleotide sequences and/or their encoded protein sequences share at least 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater sequence identity. Functions of orthologs are often highly conserved among species. Thus, isolated polynucleotides that encode R proteins and which hybridize under stringent conditions to at least one of the R proteins disclosed herein or otherwise known in the art, or to variants or fragments thereof, are encompassed by the present invention.

In one embodiment, the orthologs of the present invention have coding sequences comprising at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater nucleotide sequence identity to at least one nucleotide sequence selected from the group consisting of the nucleotide sequences set forth in SEQ ID NOS: 1, 3, 5, 6, 8, 10, 12, and 13 and/or encode proteins comprising least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater amino acid sequence identity to at least one amino acid sequence selected from the group consisting of the amino acid sequences set forth in SEQ ID NO: 2, 4, and 7.

In a PCR approach, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any plant of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.

In hybridization techniques, all or part of a known polynucleotide is used as a probe that selectively hybridizes to other corresponding polynucleotides present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism. The hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as ³²P, or any other detectable marker. Thus, for example, probes for hybridization can be made by labeling synthetic oligonucleotides based on the polynucleotides of the invention. Methods for preparation of probes for hybridization and for construction of cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

For example, an entire polynucleotide disclosed herein, or one or more portions thereof, may be used as a probe capable of specifically hybridizing to corresponding polynucleotide and messenger RNAs. To achieve specific hybridization under a variety of conditions, such probes include sequences that are unique among the sequence of the gene or cDNA of interest sequences and are optimally at least about 10 nucleotides in length, and most optimally at least about 20 nucleotides in length. Such probes may be used to amplify corresponding polynucleotides for the particular gene of interest from a chosen plant by PCR. This technique may be used to isolate additional coding sequences from a desired plant or as a diagnostic assay to determine the presence of coding sequences in a plant. Hybridization techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, for example, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

It is recognized that the R protein coding sequences of the present invention encompass polynucleotide molecules comprising a nucleotide sequence that is sufficiently identical to the nucleotide sequence of any one or more of SEQ ID NOS: 1, 3, 5, 6, 8, 10, 12, and 13. The term “sufficiently identical” is used herein to refer to a first amino acid or nucleotide sequence that contains a sufficient or minimum number of identical or equivalent (e.g., with a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have a common structural domain and/or common functional activity. For example, amino acid or nucleotide sequences that contain a common structural domain having at least about 45%, 55%, or 65% identity, preferably 75% identity, more preferably 85%, 90%, 95%, 96%, 97%, 98% or 99% identity are defined herein as sufficiently identical.

To determine the percent identity of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., percent identity=number of identical positions/total number of positions (e.g., overlapping positions)×100). In one embodiment, the two sequences are the same length. The percent identity between two sequences can be determined using techniques similar to those described below, with or without allowing gaps. In calculating percent identity, typically exact matches are counted.

The determination of percent identity between two sequences can be accomplished using a mathematical algorithm. A preferred, nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (1990) J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12, to obtain nucleotide sequences homologous to the polynucleotide molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3, to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used. BLAST, Gapped BLAST, and PSI-Blast, XBLAST and NBLAST are available on the World Wide Web at ncbi.nlm.nih.gov. Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller (1988) CABIOS 4:11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Alignment may also be performed manually by inspection.

Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using the full-length sequences of the invention and using multiple alignment by mean of the algorithm Clustal W (Nucleic Acid Research, 22(22):4673-4680, 1994) using the program AlignX included in the software package Vector NTI Suite Version 7 (InforMax, Inc., Bethesda, Md., USA) using the default parameters; or any equivalent program thereof. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by CLUSTALW (Version 1.83) using default parameters (available at the European Bioinformatics Institute website on the World Wide Web at ebi.ac.uk/Tools/clustalw/index).

The use of the term “polynucleotide” is not intended to limit the present invention to polynucleotides comprising DNA. Those of ordinary skill in the art will recognize that polynucleotides, can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. The polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.

The heterologous polynucleotides or polynucleotide constructs comprising R protein coding regions can be provided in expression cassettes for expression in the plant or other organism or non-human host cell of interest. The cassette will include 5′ and 3′ regulatory sequences operably linked to the R protein coding region. “Operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide or gene of interest and a regulatory sequence (i.e., a promoter) is functional link that allows for expression of the polynucleotide of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the R protein coding region to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.

The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a R protein coding region of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants or other organism or non-human host cell. The regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the R protein coding region or of the invention may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the R protein coding region of the invention may be heterologous to the host cell or to each other.

As used herein, “heterologous” in reference to a nucleic acid molecule, polynucleotide, nucleotide sequence, or polynucleotide construct is a nucleic acid molecule, polynucleotide, nucleotide sequence, or polynucleotide construct that originates from a foreign species, or, if from the same species, is modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.

As used herein, a “native gene” is intended to mean a gene that is a naturally-occurring gene in its natural or native position in the genome of a plant. Such a native gene has not been genetically engineered or otherwise modified in nucleotide sequence and/or positon in the genome the plant through human intervention, nor has such a native gene been introduced into the genome of the plant via artificial methods such as, for example, plant transformation.

As used herein, a “non-native gene” is intended to mean a gene that has been introduced into a plant by artificial means and/or comprises a nucleotide sequence that is not naturally occurring in the plant. Non-native genes include, for example, a gene (e.g. an R gene) that is introduced into the plant by a plant transformation method. Additionally, when a native gene in the genome of a plant is modified, for example by a genome-editing method, to comprise a nucleotide sequence that is different (i.e. non-identical) from the nucleotide sequence of native gene, the modified gene is a non-native gene.

The present invention provides host cells comprising at least of the nucleic acid molecules, expression cassettes, and vectors of the present invention. In preferred embodiments of the invention, a host cells is plant cell. In other embodiments, a host cell is selected from the group consisting of a bacterium, a fungal cell, and an animal cell. In certain embodiments, a host cell is non-human animal cell. However, in some other embodiments, the host cell is an in-vitro cultured human cell.

While it may be optimal to express the R protein using heterologous promoters, the native promoter of the corresponding R gene may be used.

The termination region may be native with the transcriptional initiation region, may be native with the operably linked R protein coding region of interest, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous to the promoter, the R protein of interest, and/or the plant host), or any combination thereof. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase (OCS) and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res. 15:9627-9639.

Where appropriate, the polynucleotides may be optimized for increased expression in the transformed plant. That is, the polynucleotides can be synthesized using plant-preferred codons for improved expression. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.

Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.

The expression cassettes may additionally contain 5′ leader sequences. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein et al. (1989) Proc. Natl. Acad. Sci. USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Gallie et al. (1995) Gene 165(2):233-238), MDMV leader (Maize Dwarf Mosaic Virus) (Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP) (Macejak et al. (1991) Nature 353:90-94); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss, New York), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al. (1991) Virology 81:382-385). See also, Della-Cioppa et al. (1987) Plant Physiol. 84:965-968.

In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.

A number of promoters can be used in the practice of the invention. The promoters can be selected based on the desired outcome. The nucleic acids can be combined with constitutive, tissue-preferred, or other promoters for expression in plants. Such constitutive promoters include, for example, the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like. Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611.

Tissue-preferred promoters can be utilized to target enhanced expression of the R protein coding sequences within a particular plant tissue. Such tissue-preferred promoters include, but are not limited to, leaf-preferred promoters, root-preferred promoters, seed-preferred promoters, and stem-preferred promoters. Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997)Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant Mol Biol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J. 4(3):495-505. Such promoters can be modified, if necessary, for weak expression.

Generally, it will be beneficial to express the gene from an inducible promoter, particularly from a pathogen-inducible promoter. Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase, chitinase, etc. See, for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et al. (1992) Plant Cell 4:645-656; and Van Loon (1985) Plant Mol. Virol. 4:111-116. See also WO 99/43819, herein incorporated by reference.

Of interest are promoters that are expressed locally at or near the site of pathogen infection. See, for example, Marineau et al. (1987) Plant Mol. Biol. 9:335-342; Matton et al. (1989) Molecular Plant-Microbe Interactions 2:325-331; Somsisch et al. (1986) Proc. Natl. Acad Sci. USA 83:2427-2430; Somsisch et al. (1988)Mol. Gen. Genet. 2:93-98; and Yang (1996) Proc. Natl. Acad Sci. USA 93:14972-14977. See also, Chen et al. (1996) Plant J. 10:955-966; Zhang et al. (1994) Proc. Natl. Acad Sci. USA 91:2507-2511; Warner et al. (1993) Plant J. 3:191-201; Siebertz et al. (1989) Plant Cell 1:961-968; U.S. Pat. No. 5,750,386 (nematode-inducible); and the references cited therein. Of particular interest is the inducible promoter for the maize PRms gene, whose expression is induced by the pathogen Fusarium moniliforme (see, for example, Cordero et al. (1992) Physiol. Mol. Plant Path. 41:189-200).

Additionally, as pathogens find entry into plants through wounds or insect damage, a wound-inducible promoter may be used in the heterologous polynucleotides of the invention. Such wound-inducible promoters include potato proteinase inhibitor (pin II) gene (Ryan (1990) Ann. Rev. Phytopath. 28:425-449; Duan et al. (1996) Nature Biotechnology 14:494-498); wun1 and wun2, U.S. Pat. No. 5,428,148; win1 and win2 (Stanford et al. (1989) Mol. Gen. Genet. 215:200-208); systemin (McGurl et al. (1992) Science 225:1570-1573); WIP1 (Rohmeier et al. (1993) Plant Mol. Biol. 22:783-792; Eckelkamp et al. (1993) FEBS Letters 323:73-76); MPI gene (Corderok et al. (1994) Plant J. 6(2):141-150); and the like, herein incorporated by reference.

Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-la promoter, which is activated by salicylic acid. Other chemical-regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.

The expression cassette can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). Additional selectable markers include phenotypic markers such as β-galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al. (2004) Biotechnol Bioeng 85:610-9 and Fetter et al. (2004) Plant Cell 16:215-28), cyan florescent protein (CYP) (Bolte et al. (2004) J. Cell Science 117:943-54 and Kato et al. (2002) Plant Physiol 129:913-42), and yellow florescent protein (PhiYFP™ from Evrogen, see, Bolte et al. (2004) J. Cell Science 117:943-54). For additional selectable markers, see generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-511; Christopherson et al. (1992) Proc. Natl. Acad Sci. USA 89:6314-6318; Yao et al. (1992) Cell 71:63-72; Reznikoff (1992) Mol. Microbiol. 6:2419-2422; Barkley et al. (1980) in The Operon, pp. 177-220; Hu et al. (1987) Cell 48:555-566; Brown et al. (1987) Cell 49:603-612; Figge et al. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natl. Acad Aci. USA 86:5400-5404; Fuerst et al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553; Deuschle et al. (1990) Science 248:480-483; Gossen (1993) Ph.D. Thesis, University of Heidelberg; Reines et al. (1993) Proc. Natl. Acad Sci. USA 90:1917-1921; Labow et al. (1990) Mol. Cell. Biol. 10:3343-3356; Zambretti et al. (1992) Proc. Natl. Acad Sci. USA 89:3952-3956; Baim et al. (1991) Proc. Natl. Acad. Sci. USA 88:5072-5076; Wyborski et al. (1991) Nucleic Acids Res. 19:4647-4653; Hillenand-Wissman (1989) Topics Mol. Struc. Biol. 10:143-162; Degenkolb et al. (1991) Antimicrob. Agents Chemother. 35:1591-1595; Kleinschnidt et al. (1988) Biochemistry 27:1094-1104; Bonin (1993) Ph.D. Thesis, University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad Sci. USA 89:5547-5551; Oliva et al. (1992) Antimicrob. Agents Chemother. 36:913-919; Hlavka et al. (1985) Handbook of Experimental Pharmacology, Vol. 78 (Springer-Verlag, Berlin); Gill et al. (1988) Nature 334:721-724. Such disclosures are herein incorporated by reference.

The above list of selectable marker genes is not intended to be limiting. Any selectable marker gene can be used in the present invention.

Numerous plant transformation vectors and methods for transforming plants are available. See, for example, An, G. et al. (1986) Plant Pysiol., 81:301-305; Fry, J., et al. (1987) Plant Cell Rep. 6:321-325; Block, M. (1988) Theor. Appl Genet. 76:767-774; Hinchee, et al. (1990) Stadler. Genet. Symp. 203212.203-212; Cousins, et al. (1991) Aust. J. Plant Physiol. 18:481-494; Chee, P. P. and Slightom, J. L. (1992) Gene. 118:255-260; Christou, et al. (1992) Trends. Biotechnol. 10:239-246; D'Halluin, et al. (1992) Bio/Technol. 10:309-314; Dhir, et al. (1992) Plant Physiol. 99:81-88; Casas et al. (1993) Proc. Nat. Acad Sci. USA 90:11212-11216; Christou, P. (1993) In Vitro Cell. Dev. Biol.-Plant; 29P:119-124; Davies, et al. (1993) Plant Cell Rep. 12:180-183; Dong, J. A. and Mchughen, A. (1993) Plant Sci. 91:139-148; Franklin, C. I. and Trieu, T. N. (1993) Plant. Physiol. 102:167; Golovkin, et al. (1993) Plant Sci. 90:41-52; Guo Chin Sci. Bull. 38:2072-2078; Asano, et al. (1994) Plant Cell Rep. 13; Ayeres N. M. and Park, W. D. (1994) Crit. Rev. Plant. Sci. 13:219-239; Barcelo, et al. (1994) Plant. J. 5:583-592; Becker, et al. (1994) Plant. J. 5:299-307; Borkowska et al. (1994) Acta. Physiol Plant. 16:225-230; Christou, P. (1994) Agro. Food. Ind. Hi Tech. 5: 17-27; Eapen et al. (1994) Plant Cell Rep. 13:582-586; Hartman, et al. (1994) Bio-Technology 12: 919923; Ritala, et al. (1994) Plant. Mol. Biol. 24:317-325; and Wan, Y. C. and Lemaux, P. G. (1994) Plant Physiol. 104:3748.

The methods of the invention involve introducing a heterologous polynucleotide or polynucleotide construct into a plant. By “introducing” is intended presenting to the plant the heterologous polynucleotide or polynucleotide construct in such a manner that the construct gains access to the interior of a cell of the plant. The methods of the invention do not depend on a particular method for introducing a heterologous polynucleotide or polynucleotide construct to a plant, only that the heterologous polynucleotide or polynucleotide construct gains access to the interior of at least one cell of the plant. Methods for introducing heterologous polynucleotides or polynucleotide constructs into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.

By “stable transformation” is intended that the heterologous polynucleotide or polynucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by progeny thereof. By “transient transformation” is intended that a heterologous polynucleotide or polynucleotide construct introduced into a plant does not integrate into the genome of the plant. It is recognized that stable and transient transformation methods comprise introducing one or more nucleic acid molecules (e.g. DNA), particularly one or more recombinant nucleic acid molecules (e.g. recombinant DNA) into a plant, plant cell, or other host cell or organism.

For the transformation of plants and plant cells, the nucleotide sequences of the invention are inserted using standard techniques into any vector known in the art that is suitable for expression of the nucleotide sequences in a plant or plant cell. The selection of the vector depends on the preferred transformation technique and the target plant species to be transformed.

Methodologies for constructing plant expression cassettes and introducing foreign nucleic acids into plants are generally known in the art and have been previously described. For example, foreign DNA can be introduced into plants, using tumor-inducing (Ti) plasmid vectors.

Other methods utilized for foreign DNA delivery involve the use of PEG mediated protoplast transformation, electroporation, microinjection whiskers, and biolistics or microprojectile bombardment for direct DNA uptake. Such methods are known in the art. (U.S. Pat. No. 5,405,765 to Vasil et al.; Bilang et al. (1991) Gene 100: 247-250; Scheid et al., (1991) Mol. Gen. Genet., 228: 104-112; Guerche et al., (1987) Plant Science 52: 111-116; Neuhause et al., (1987) Theor. Appl Genet. 75: 30-36; Klein et al., (1987) Nature 327: 70-73; Howell et al., (1980) Science 208:1265; Horsch et al., (1985) Science 227: 1229-1231; DeBlock et al., (1989) Plant Physiology 91: 694-701; Methods for Plant Molecular Biology (Weissbach and Weissbach, eds.) Academic Press, Inc. (1988) and Methods in Plant Molecular Biology (Schuler and Zielinski, eds.) Academic Press, Inc. (1989). The method of transformation depends upon the plant cell to be transformed, stability of vectors used, expression level of gene products and other parameters.

Other suitable methods of introducing nucleotide sequences into plant cells and subsequent insertion into the plant genome include microinjection as Crossway et al. (1986) Biotechniques 4:320-334, electroporation as described by Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediated transformation as described by Townsend et al., U.S. Pat. No. 5,563,055, Zhao et al., U.S. Pat. No. 5,981,840, direct gene transfer as described by Paszkowski et al. (1984) EMBO J. 3:2717-2722, and ballistic particle acceleration as described in, for example, Sanford et al., U.S. Pat. No. 4,945,050; Tomes et al., U.S. Pat. No. 5,879,918; Tomes et al., U.S. Pat. No. 5,886,244; Bidney et al., U.S. Pat. No. 5,932,782; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology 6:923-926); and Lec transformation (WO 00/28058). Also see, Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987) Particulate Science and Technology 5:27-37 (onion); Christou et al. (1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio Technology 6:923-926 (soybean); Finer and McMullen (1991) In Vitro Cell Dev. Biol. 27P:175-182 (soybean); Singh et al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736-740 (rice); Klein et al. (1988) Proc. Natl. Acad. Sci. USA 85:4305-4309 (maize); Klein et al. (1988) Biotechnology 6:559-563 (maize); Tomes, U.S. Pat. No. 5,240,855; Buising et al., U.S. Pat. Nos. 5,322,783 and 5,324,646; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg (Springer-Verlag, Berlin) (maize); Klein et al. (1988) Plant Physiol. 91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839 (maize); Hooykaas-Van Slogteren et al. (1984) Nature (London) 311:763-764; Bowen et al., U.S. Pat. No. 5,736,369 (cereals); Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349 (Liliaceae); De Wet et al. (1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, New York), pp. 197-209 (pollen); Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet. 84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992) Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports 12:250-255 and Christou and Ford (1995) Annals ofBotany 75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens); all of which are herein incorporated by reference.

The polynucleotides of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids. Generally, such methods involve incorporating a heterologous polynucleotide or polynucleotide construct of the invention within a viral DNA or RNA molecule. Further, it is recognized that promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotide constructs into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367 and 5,316,931; herein incorporated by reference.

If desired, the modified viruses or modified viral nucleic acids can be prepared in formulations. Such formulations are prepared in a known manner (see e.g. for review U.S. Pat. No. 3,060,084, EP-A 707 445 (for liquid concentrates), Browning, “Agglomeration”, Chemical Engineering, Dec. 4, 1967, 147-48, Perry's Chemical Engineer's Handbook, 4th Ed., McGraw-Hill, New York, 1963, pages 8-57 and et seq. WO 91/13546, U.S. Pat. Nos. 4,172,714, 4,144,050, 3,920,442, 5,180,587, 5,232,701, 5,208,030, GB 2,095,558, U.S. Pat. No. 3,299,566, Klingman, Weed Control as a Science, John Wiley and Sons, Inc., New York, 1961, Hance et al. Weed Control Handbook, 8th Ed., Blackwell Scientific Publications, Oxford, 1989 and Mollet, H., Grubemann, A., Formulation technology, Wiley VCH Verlag GmbH, Weinheim (Germany), 2001, 2. D. A. Knowles, Chemistry and Technology of Agrochemical Formulations, Kluwer Academic Publishers, Dordrecht, 1998 (ISBN 0-7514-0443-8), for example by extending the active compound with auxiliaries suitable for the formulation of agrochemicals, such as solvents and/or carriers, if desired emulsifiers, surfactants and dispersants, preservatives, antifoaming agents, anti-freezing agents, for seed treatment formulation also optionally colorants and/or binders and/or gelling agents.

In specific embodiments, the polynucleotides, polynucleotide constructs, and expression cassettes of the invention can be provided to a plant using a variety of transient transformation methods known in the art. Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol Gen. Genet. 202:179-185; Nomura et al. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) PNAS Sci. 91: 2176-2180 and Hush et al. (1994) J. Cell Science 107:775-784, all of which are herein incorporated by reference. Alternatively, the polynucleotide can be transiently transformed into the plant using techniques known in the art. Such techniques include viral vector system and Agrobacterium tumefaciens-mediated transient expression as described elsewhere herein.

The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a heterologous polynucleotide or polynucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.

Any methods known in the art for modifying DNA in the genome of a plant can be used to modify genomic nucleotide sequences in planta, for example, to create or insert a resistance gene or even to replace or modify an endogenous resistance gene or allele thereof. Such methods include, but are not limited to, genome-editing (or gene-editing) techniques, such as, for example, methods involving targeted mutagenesis, homologous recombination, and mutation breeding. Targeted mutagenesis or similar techniques are disclosed in U.S. Pat. Nos. 5,565,350; 5,731,181; 5,756,325; 5,760,012; 5,795,972, 5,871,984, and 8,106,259; all of which are herein incorporated in their entirety by reference. Methods for gene modification or gene replacement comprising homologous recombination can involve inducing double breaks in DNA using zinc-finger nucleases (ZFN), TAL (transcription activator-like) effector nucleases (TALEN), Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated nuclease (CRISPR/Cas nuclease), or homing endonucleases that have been engineered endonucleases to make double-strand breaks at specific recognition sequences in the genome of a plant, other organism, or host cell. See, for example, Durai et al., (2005) Nucleic Acids Re.s 33:5978-90; Mani et al. (2005) Biochem. Biophys. Res. Comm. 335:447-57; U.S. Pat. Nos. 7,163,824, 7,001,768, and 6,453,242; Arnould et al. (2006) J. Mol. Biol. 355:443-58; Ashworth et al., (2006) Nature 441:656-9; Doyon et al. (2006) J. Am. Chem. Soc. 128:2477-84; Rosen et al., (2006) Nucleic Acids Res. 34:4791-800; and Smith et al., (2006) Nucleic Acids Res. 34:e149; U.S. Pat. App. Pub. No. 2009/0133152; and U.S. Pat. App. Pub. No. 2007/0117128; all of which are herein incorporated in their entirety by reference.

Unless stated otherwise or apparent from the context of a use, the term “gene replacement” is intended to mean the replacement of any portion of a first polynucleotide molecule or nucleic acid molecule (e.g. a chromosome) that involves homologous recombination with a second polynucleotide molecule or nucleic acid molecule using a genome-editing technique as disclosed elsewhere herein, whereby at least a part of the nucleotide sequence of the first polynucleotide molecule or nucleic acid molecule is replaced with the second polynucleotide molecule or nucleic acid molecule. It is recognized that such gene replacement can result in additions, deletions, and/or modifications in the nucleotide sequence of the first polynucleotide molecule or nucleic acid molecule and can involve the replacement of an entire gene or genes, the replacement of any part or parts of one gene, or the replacement of non-gene sequences in the first polynucleotide molecule or nucleic acid molecule.

TAL effector nucleases (TALENs) can be used to make double-strand breaks at specific recognition sequences in the genome of a plant for gene modification or gene replacement through homologous recombination. TAL effector nucleases are a class of sequence-specific nucleases that can be used to make double-strand breaks at specific target sequences in the genome of a plant or other organism. TAL effector nucleases are created by fusing a native or engineered transcription activator-like (TAL) effector, or functional part thereof, to the catalytic domain of an endonuclease, such as, for example, FokI. The unique, modular TAL effector DNA binding domain allows for the design of proteins with potentially any given DNA recognition specificity. Thus, the DNA binding domains of the TAL effector nucleases can be engineered to recognize specific DNA target sites and thus, used to make double-strand breaks at desired target sequences. See, WO 2010/079430; Morbitzer et al. (2010) PNAS 10.1073/pnas.1013133107; Scholze & Boch (2010) Virulence 1:428-432; Christian et al. Genetics (2010) 186:757-761; Li et al. (2010) Nuc. Acids Res. (2010) doi:10.1093/nar/gkg704; and Miller et al. (2011) Nat. Biotechnol. 29:143-148; all of which are herein incorporated by reference.

The CRISPR/Cas nuclease system can also be used to make double-strand breaks at specific recognition sequences in the genome of a plant for gene modification or gene replacement through homologous recombination. The CRISPR/Cas nuclease is an RNA-guided (simple guide RNA, sgRNA in short) DNA endonuclease system performing sequence-specific double-stranded breaks in a DNA segment homologous to the designed RNA. It is possible to design the specificity of the sequence (Cho S. W. et al., Nat. Biotechnol. 31:230-232, 2013; Cong L. et al., Science 339:819-823, 2013; Mali P. et al., Science 339:823-826, 2013; Feng Z. et al., Cell Research 1-4, 2013).

In addition, a ZFN can be used to make double-strand breaks at specific recognition sequences in the genome of a plant for gene modification or gene replacement through homologous recombination. The Zinc Finger Nuclease (ZFN) is a fusion protein comprising the part of the FokI restriction endonuclease protein responsible for DNA cleavage and a zinc finger protein which recognizes specific, designed genomic sequences and cleaves the double-stranded DNA at those sequences, thereby producing free DNA ends (Urnov et al. (2010) Nat. Rev. Genet. 11:636-46; Carroll (2011) Genetics. 188:773-82).

Breaking DNA using site specific nucleases, such as, for example, those described herein above, can increase the rate of homologous recombination in the region of the breakage. Thus, coupling of such effectors as described above with nucleases enables the generation of targeted changes in genomes which include additions, deletions and other modifications.

The nucleic acid molecules, expression cassettes, vectors, and heterologous polynucleotides of the present invention may be used for transformation and/or genome editing of any plant species, including, but not limited to, monocots and dicots.

As used herein, the term “plant” includes seeds, plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, tubers, propagules, leaves, flowers, branches, fruits, roots, root tips, anthers, and the like. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides. As used herein, “progeny” and “progeny plant” comprise any subsequent generation of a plant whether resulting from sexual reproduction and/or asexual propagation, unless it is expressly stated otherwise or is apparent from the context of usage.

As used herein, the terms “transgenic plant” and “transformed plant” are equivalent terms that refer to a “plant” as described above, wherein the plant comprises a heterologous nucleic acid molecule, heterologous polynucleotide, or heterologous polynucleotide construct that is introduced into a plant by, for example, any of the stable and transient transformation methods disclosed elsewhere herein or otherwise known in the art. Such transgenic plants and transformed plants also refer, for example, the plant into which the heterologous nucleic acid molecule, heterologous polynucleotide, or heterologous polynucleotide construct was first introduced and also any of its progeny plants that comprise the heterologous nucleic acid molecule, heterologous polynucleotide, or heterologous polynucleotide construct.

In certain embodiments of the invention, the methods involve the planting of seedlings and/or tubers and then growing such seedlings and tubers so as to produce plants derived therefrom and optionally harvesting from the plants a plant part or parts. As used herein, a “seedling” refers to a less than fully mature plant that is typically grown in greenhouse or other controlled- or semi-controlled (e.g. a cold frame) environmental conditions before planting or replanting outdoors or in a greenhouse for the production a harvestable plant part, such as, for example, a tomato fruit, a potato tuber or a tobacco leaf. As used herein, a “tuber” refers to an entire tuber or part or parts thereof, unless stated otherwise or apparent from the context of use. A preferred tuber of the present invention is a potato tuber.

In the methods of the invention involving planting a tuber, a part of tuber preferably comprises a sufficient portion of the tuber whereby the part is capable of growing into a plant under favorable conditions for the growth and development of a plant derived from the tuber. It is recognized that such favorable conditions for the growth and development of crop plants, particularly solanaceous crop plants, are generally known in the art.

In some embodiments of the present invention, a plant cell is transformed with a heterologous polynucleotide encoding an R protein of the present invention. The term “expression” as used herein refers to the biosynthesis of a gene product, including the transcription and/or translation of said gene product. The “expression” or “production” of a protein or polypeptide from a DNA molecule refers to the transcription and translation of the coding sequence to produce the protein or polypeptide, while the “expression” or “production” of a protein or polypeptide from an RNA molecule refers to the translation of the RNA coding sequence to produce the protein or polypeptide. Examples of heterologous polynucleotides and nucleic acid molecules that encode R proteins are described elsewhere herein.

The use of the terms “DNA” or “RNA” herein is not intended to limit the present invention to polynucleotide molecules comprising DNA or RNA. Those of ordinary skill in the art will recognize that the methods and compositions of the invention encompass polynucleotide molecules comprised of deoxyribonucleotides (i.e., DNA), ribonucleotides (i.e., RNA) or combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues including, but not limited to, nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs). The polynucleotide molecules of the invention also encompass all forms of polynucleotide molecules including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like. Furthermore, it is understood by those of ordinary skill in the art that the nucleotide sequences disclosed herein also encompasses the complement of that exemplified nucleotide sequence.

The invention is drawn to compositions and methods for enhancing the resistance of a plant to plant disease, particularly to compositions and methods for enhancing the resistance of a plant to a plant disease caused by at least one potyvirus. By “disease resistance” is intended that the plants avoid the disease symptoms that are the outcome of plant-pathogen interactions. That is, pathogens are prevented from causing plant diseases and the associated disease symptoms, or alternatively, the disease symptoms caused by the pathogen is minimized or lessened.

The following examples are offered by way of illustration and not by way of limitation.

EXAMPLES Example 1: Mapping of Ry_(sto) Gene from dH Alicja

To clone the Ry_(sto) gene, we developed a diploid potato (2n=2x=24) mapping population by a cross between PVY-resistant, heterozygous dihaploid clone dH Alicja, and susceptible, diploid clone 83-3121. dH Alicja was obtained from potato cultivar Alicja via parthenogenesis.

The extreme resistance (ER) to PVY in dH Alicja was conferred by the gene Ry_(sto) which was derived from clone MPI 55.957154. The Ry_(sto) gene in MPI 55.957154 was derived from a Solanum stoloniferum accession that is in the pedigree MPI 55.957/54. This S. stoloniferum accession was from the wild Solanum spp. collection of Max Planck Institute (Ross (1958) “Resistenz züchtung gegen die Mosaik-und andere Viren der Kartoffel,” in Handbuch der Pflanzenzuchtung, 2^(nd) ed., Vol. III, Kappert and Rudorf, eds., Paul Parey, Berlin, pp 106-125).

The mapping population consisted of 391 F1 individuals, and was evaluated for resistance to PVY as described by Flis et al. ((2005) Molecular Breeding 15:95-101). The segregation ratio of resistant versus susceptible progeny in the mapping population deviated from the 1:1 ratio expected for the segregation of a single dominant gene and was distorted towards resistance (149 susceptible and 242 PVY-resistant F1 individuals).

Example 2: SMRT RenSeq Combined with Bulked Segregant Analysis (BSA) RenSeq on 160 Susceptible Plants Yields 12 Candidate Genes

We hypothesized that the underlying PVY resistance genes encode a nucleotide binding-leucine rich repeat (NLR) protein. To predict candidate gene(s) for Ry_(sto), we applied R gene enrichment and sequencing (RenSeq) combined with Illumina MiSeq 250 PE sequencing to 149 bulked susceptible plants from mapping population (BS), alongside with susceptible (S) and resistant (R) parent. RenSeq (Jupe et al. (2013) Plant J. 76:530-544) is a method which allows one to capture and sequence all NLR-type of resistance genes in plants. We employed an SMRT RenSeq, an improved version of RenSeq, that enables one to prepare long, enriched libraries that are suitable for using Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. Combined with bulked segregant analysis (Michelmore et al. (1991) PNAS 88:9828-9823) and long-read sequencing, like the PacBio platform (“SMRT RenSeq”) (Witek et al. (2016) Nat. Biotechnol. 34:656-660), SMRT RenSeq allows one to quickly predict a set of candidate genes without a necessity of developing and screening large mapping population or building BAC libraries. To generate high confidence de novo assembly of R-parent NLRs, we also carried out SMRT RenSeq on gDNA derived from the resistant clone dH Alicja. Reads obtained from SMRT RenSeq were assembled using Geneious 8.1.2 software as described previously (Witek et al. (2016) Nat. Biotechnol. 34: 656-660), resulting in 1,555 contigs. R, S and BS reads from Illumina 250PE were mapped to contigs derived from SMRT RenSeq assembly using BWA (Li & Durbin (2009) Bioinformatics 25:1754-1760), with default settings. SNP calling and candidate prediction was performed as described previously in Jupe et al. ((2013) Plant J. 76:530-544) and Witek et al. ((2016) Nat. Biotechnol. 34:656-660). Additionally, we looked for candidate NLRs showing presence/absence polymorphism between R and S parent, and linkage to resistance based on BS samples. Numbers of pair-end mapped reads to contigs derived from SMRT RenSeq assembly were calculated using TSL Galaxy built-in scripts (MacLean & Kamoun (2012) Nat. Biotechnol. 30:33-34) for each R, S and BS samples. Resulting data were sorted and visualized in Microsoft Excel software. As a presence/absence polymorphism, we considered contigs with at least 250 mapped reads from R parent, and less than 10% and 18% of that number for S and BS samples, respectively.

SNP calling and presence/absence polymorphism detection resulted in 12 candidate NLR genes linked to Ry_(sto) resistance. Expression of all candidate genes was confirmed using cDNA data from R parent as described previously (Andolfo et al. (2016) BMC Plant Biol. 14:1-12; Witek et al. (2016) Nat. Biotechnol. 34:656-660). Four candidate genes belonged to coiled-coil (CC) class of NLR family (CNL), and remaining eight to Toll/interleukin-1 receptor homology (TIR) domain-containing NLRs (TNL). Interestingly, when using BWA mapping criteria described above, all NLR genes linked to Ry resistance show presence/absence polymorphism, what indicates that the whole interval was introgressed from S. stoloniferum.

Example 3: Comparative Analysis Identifies the Same NLRs as Candidate Genes for Ry_(sto)

Several studies positioned Ry resistance gene from S. stoloniferum on the most distal end of the long arm of chromosome 12 (Flis et al. (2005) Molecular Breeding 15:95-101; Song et al. (2005) Theor. Appl. Genet. 111:879-87; van Eck et al. (2017) Theor. Appl. Genet. 130:515-528), what corresponds to the region downstream of 58 Mb in the reference potato genome clone DM (The Potato Genome Sequencing Consortium (2011) Nature 475:189-195). This region contains 18 complete and partial NLR immune receptors from both CNL and TNL groups (Jupe et al. (2013) Plant J 76:530-544). To identify the homologue sequences of these NLRs from dH Alicja (putative Ry_(sto) gene), we looked for NLRs in SMRT RenSeq assembly as described by Witek et al. ((2016) Nat. Biotechnol. 34:656-660). We identified 33 NLRs, including all 12 NLRs previously detected as linked using RenSeq data. The remaining 21 genes did not show any linked polymorphism in RenSeq data, thus suggesting that they are in repulsion phase or are not linked. This in silico analysis pointed out that all selected candidates from SMRT RenSeq data localize to the distal end of chromosome 12, the same region where Ry_(sto) was previously positioned.

Example 4: Transient Expression of Nine Expressed NLR Genes in Nicotiana benthamiana Reveals Two that can Restrict Virus Multiplication

We cloned the predicted coding sequences of 9 candidate genes into a binary expression vector under control of 35S promoter, and transformed them into Agrobacterium as described by Witek et al. ((2016) Nat. Biotechnol. 34:656-660). These constructs were transiently expressed in Nicotiana benthamiana leaves by infiltrating Agrobacterium suspension at an absorbance (OD₆₀₀) of about 1.0, followed by PVY^(NTN) (isolate NIB-NTN; GenBank: AJ585342.1) inoculation as described by Yin et al. ((2012) J. Plant Prot. Res 52: 214-19). Seven days after infection leaf samples were collected and levels of viral mRNA were measured with quantitative-RT-PCR as described previously by Pompe-Novak et al. ((2006) Physiol. Mol. Plant. Pathol. 67:237-47). This analysis showed that two of the candidate genes, namely c630 and c516 (SEQ ID NO: 1 and SEQ ID NO: 6, respectively), under the control of 35S promoter reduced virus multiplication and spreading compared to WT N. benthamiana plants and remaining candidate contigs (FIGS. 1A and 1 i). Transient delivery of candidate c630 under its native promoter (over 2 kb, nucleotides 257 to 2518 of SEQ ID NO: 1) and terminator elements (over 1 kb for splice variant 1, nucleotides 6732 to 7745 and over 0.45 kb for splice variant 2, nucleotides 7280 to 7745, of SEQ ID NO: 1), followed by PVY infection, showed the same level of virus multiplication inhibition as the 35S::c630 construct (FIG. 1A).

We further tested the functionality of candidate contigs c630 and c516 by infiltrating them into N. benthamiana plants systemically infected with PVY^(NTN) (isolate NIB-NTN) or PVX virus. Only the infiltration of c630 into plants carrying PVY^(NTN) resulted in HR (FIG. 2, left), similar to a HR in control experiment, where Rx gene (Bendahmane et al. (1999) Plant Cell 5:781-791) was delivered to plants infected with PVX virus (FIG. 2, right). Infiltration of c516 or Rx into PVY^(NTN) carrying plants did not result in visible symptoms of cell death (data not shown).

Example 5: c630 Recognizes Multiple Strains of PVY

To test if c630 and c516 can recognize other strains of PVY virus, we infected N. benthamiana plants with PVY isolates 0, N, N-Wilga, NIB-NTN and unrelated viruses (PVX and TMV(U1)) as controls. Two weeks later, leaves showing symptoms of viral infection were infiltrated with Agrobacterium carrying candidate contigs c630, c516 and an empty plasmid. Whereas infiltration of c516 only resulted in a weak HR in plants carrying less aggressive PVY strains 0 and N, c630 infiltration resulted in a strong HR in plants carrying all PVY strains (but not control PVX or TMV) (Table 2). No cell death was observed when plants were infiltrated with Agrobacterium carrying an empty vector. These experiments further verified contigs c630 and c516 as candidates for the functional Ry_(sto) gene.

TABLE 2 Strength* of HR After Agrobacterium Transient Delivery of Various Constructs into N. benthamiana Plants Systemically Infected with PVY, PVX or TMV Viruses Virus 35S::c516 35S::c630 empty vector 0 (LW) + ++ − N (Ny) +/− ++ − N-Wilga − ++ − NIB-NTN − ++ − PVX (strain 0) − − − TMV (U1) − − − *Strength of HR response: − no HR; +/− weak HR; + HR (5 dpi); ++ strong HR (3 dpi).

Example 6: Nicotiana tabacum Plants Stably Transformed with c630 Restrict Systemic PVY Spread

We constructed stable transgenic Nicotiana tabacum cv. Xanthi nc plants carrying candidate genes c630 and c516 under the control of 35S promoter or native regulatory elements, using Agrobacterium (strain LBA 4404) transformation method described in Horsch et al. ((1985) Science 227:1229-1231).

Seven-week-old N. tabacum 35S transgenic and WT control plants were inoculated with PVY^(NTN) (isolate NIB-NTN) or mock treated with water. Five days after PVY inoculation, large necrotic spots were visible on all eight transgenic plants carrying c630 candidate gene (FIG. 3, left panel), while no macroscopic symptoms could be observed on WT plants (FIG. 3, right panel) or c516 transgenic (data not shown). While typical mosaic symptoms of PVY infection were observed at14 dpi on WT-control (FIG. 4, bottom panel) and c516 plants, transgenic plants carrying c630 remained either symptomless for PVY (lines A, B, E; FIG. 4, top panel) or showed severe infections symptoms on upper leaves leading to systemic necrotization (lines C, D, F, G and H; FIG. 5). We speculated that the latter had partial resistance that resulted in systemic virus spread, HR of veins and ultimately death of the whole plants. Quantitative RT-PCR on upper, non-inoculated leaves of stable transgenic plants showed that systemic spread of the virus was fully restricted in lines A, B and E which remained symptomless for PVY (FIG. 6A), while viral mRNA levels in remaining transgenic plants were comparable to WT controls. These results were confirmed in F1 generation (FIG. 6B). Interestingly, in tobacco plants infected and maintained at elevated temperature (32° C.), candidate gene c630 was still preventing systemic infection. This result is consistent with findings that ER conferred by Ry-f_(sto) is temperature independent (Flis et al. (2005) Molecular Breeding 15:95-101).

In four out of seven lines transformed with c630 candidate gene under control of native regulatory elements, we observed a local response at 7 dpi similar to that in 35S::c630 transgenic plants, and systemic leaves did not show any macroscopic symptoms. The absence of virus was confirmed with quantitative RT-PCR at 7 and 14 dpi. In three lines where expression of transgene was not detectable or low, PVY spread was not restricted (FIG. 7).

These results demonstrated that c630 can restrict systemic virus spreading in stable transgenic tobacco plants when expressed under both 35S and native regulatory elements.

Example 7: Solanum tuberosum Plants Stably Transformed with c630 Under the Control of 35S Promoter Restrict Systemic PVY Spread

We constructed stable transgenic Solanum tuberosum cv. Maris Piper (MP) and cv. Russet Burbank (RB) plants carrying gene c630 under the control of 35S promoter and native regulatory elements, using the transformation method described in Mac et al. ((2004) Cellular and Molecular Biology Letters 9:843-53). Transgenic plants were infected with PVY^(NTN) and virus spreading was monitored in upper, non-inoculated leaves 21 dpi using ELISA test with antibodies specific to PVY. In 10 out of 12 transgenic plants with the Maris Piper background that were tested, PVY was not detected (see Table 3); lack of virus was confirmed in 6wpi in three transgenic lines (A, F and N, Table 4). We additionally tested three transgenic lines (one susceptible, two resistant) using qPCR, which confirmed the results from ELISA test. The inhibition of virus multiplication and spreading in two resistant transgenic plants correlated with detectable levels of expression of the gene c630. In susceptible transgenic plants, the expression of the transgene was not detected.

TABLE 3 PVY Detection Using ELISA Test in Systemic Leaves of MP Plants Transformed with 35S::c630 Line name OD₅₅₀ Phenotype MP WT 1.917 S N. tabacum 630A 0.012 R N. tabacum 630E 0.002 R MP 630A* 0.019 R MP 630B 0.010 R MP 630C 0.006 R MP 630F 0.007 R MP 630H* 1.706 S MP 630K* 0.013 R MP 630N 0.003 R MP 630P 0.015 R MP 630 R 0.022 R MP 630T 0.011 R MP 630Z 1.956 S WT MP was used as a susceptible control, and two lines of N. tabacum/35S::c630 (A and E) as resistant controls. Table shows average values from three plants for all MP lines except for F and Z, where two plants were tested. The absorbance was measured at a wavelength of 550 nm (OD₅₅₀). Asterisk indicates lines where presence (S phenotype) and absence (R phenotype) of the virus was validated with qPCR.

Similar results were obtained in a Russet Burbank background, where in all four tested transgenic lines carrying gene c630 under the control of 35S promoter, lack of PVY was confirmed with ELISA test (Table 4) and quantitative RT-PCR (FIG. 9) in systemic, non-inoculated leaves at 3 wpi. Additionally, since 11 dpi, we observed strong chlorosis symptoms on infected leaves of wild-type plants, while infected leaves of transgenic plants remained symptomless till at least 3 wpi (FIG. 8).

These results confirmed that c630 is conferring ER-type of resistance against PVY in stable transgenic potato lines cv. Maris Piper and Russet Burbank when expressed under 35S promoter and is a functional Ry_(sto) resistance gene.

TABLE 4 PVY Detection Using ELISA Test in Systemic Leaves of RB Plants Transformed with 35S::c630 Line name OD₅₅₀ Phenotype MP WT mock 0.046 R MP WT 2.495 S RB WT 0.878 S MP 630A (6 wpi) 0.002 R MP 630F (6 wpi) 0.000 R MP 630N (6 wpi) 0.000 R RB 630A 0.006 R RB 630B 0.010 R RB 630C 0.006 R RB 630D 0.003 R WT MP and RB lines were used as a susceptible controls, and three lines of S. tuberosum/35S::c630 (A, F, N) as resistant controls (6wpi). Table shows average values from three plants for RB lines except A and B, average value from two plants for line D and single measurement for line C. The absorbance was measured at a wavelength of 550 nm (OD₅₅₀). Column three indicates plant phenotypes; S—susceptible, R—resistant.

Example 8: Solanum tuberosum Plants Stably Transformed with c630 Expressed Under Native Regulatory Sequences Restrict Systemic PVY Spread

Stable transgenic Solanum tuberosum cv. Maris Piper plants expressing c630 under its native regulatory sequences were generated as described in Example 7. Four-week-old transgenic plants were infected with PVY^(NTN) as described in Example 7. Three weeks after PVY inoculation, mRNA was isolated from upper, non-inoculated leaves. The PVY mRNA levels and the expression of c630 were quantified with qPCR, relative to the EF1 and Sec3 reference genes and expressed as means±SD calculated from three biological replicates per plant line. No PVY was detected in 5 lines expressing c630 (FIGS. 10A-10B).

The results shown in FIGS. 10A-10B demonstrate that the expression of c630 under control of its native regulatory sequences in potato plants from stable transgenic potato lines restricts systemic PVY spread in such plants.

Example 9: Nicotiana tabacum Plants Stably Transformed with c630 Restrict Systemic PVA Spread

It was shown by Barker et al. ((1996) Theor. Appl. Genet. 93:710-716) that resistance to Potato virus A (PVA) is linked to PVY resistance mediated by Ry-f_(sto). To test whether c630 also mediates resistance against PVA, we inoculated Nicotiana tabacum/35S::c630 plants with two strains of PVA (strains SASA and X Bonin). After 7 dpi, we observed HR on infected leaves of tobacco plants carrying 35S::c630 construct, and there was no local response in control tobacco plants for both the plants inoculated with SASA and X Bonin. FIG. 11 illustrates the results for leaves inoculated with SASA at 7 dpi. Similar results were obtained with leaves inoculated with X Bonin (not shown). Additionally, by 7 dpi, upper non-inoculated leaves of control plants showed typical mosaic symptoms of PVA infection and also stunted growth, while the N. tabacum/35S::c630 stably transformed plants remained healthy till at least 21 dpi (not shown). Western blotting analysis with anti-PVA antibodies and qPCR confirmed inhibition of PVA systemic spreading (not shown). These results demonstrate that c630 can confer resistance against multiple strains of PVA in addition to conferring resistance against multiple strains of PVY as disclosed above.

Upper non-inoculated leaves of control and transgenic plants carrying 35S::c630 are being tested for the presence of PVA using specific antibodies after 7, 14 and 21 dpi.

Example 10: c630 Undergoes Alternative Splicing

To annotate the coding sequence (CDS) of c630, we mapped RenSeq cDNA reads generated from R parent using TopHat (Trapnell et al. (2009) Bionformatics 25:1105-1111) with default settings. Mapping pattern suggests that the gene c630 undergoes alternative splicing and two splice forms differing at 3′ end can be distinguished. The dominant transcript variant consists of 4 exons (SEQ ID NO: 3) encoding 1,105 amino acids (SEQ ID NO: 2), and is supported by 78-87% cDNA reads. Remaining reads support the presence of an additional intron at 3′ end, starting 27 nucleotides (nt) upstream of STOP codon of splice variant 1, followed by additional exon encoding 162 amino acids (splice variant 2, SEQ ID NO: 5) resulting a total encoded protein length of 1,258 amino acids (SEQ ID NO: 4). The gene encoded by c630 has motifs and domains typical for TNL type of resistance gene; namely a TIR domain, followed by nucleotide binding (NB-ARC) domain and multiple leucine-reach repeats (LRR). Both splice variants share less than 34% identity on amino acid level with previously described TNL type resistance proteins from Solanum spp., including N (GeneBank: Q40392), Y-1 (GeneBank: CAC82812), Bs4 (GeneBank: AY438027), Grol-4 (GeneBank: AAP44390) and Pvr4 (GeneBank: KT359375), see Table 5.

TABLE 5 Full-length Amino Acid Identity (%) Between c630 (splice variant one) and Functional Solanaceae TNL Resistance Proteins c630 Gro1-4 Y-1 Bs4 N Pvr4 c630 33.3 31.7 31.7 32.2 9.2 Gro1-4 34.4 36.1 35.7 10.4 Y-1 57.9 55.3 9.0 Bs4 55.0 8.6 N 9.7 Pvr4

The article “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one or more element.

Throughout the specification the word “comprising,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.

All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims. 

That which is claimed:
 1. A method for identifying a solanaceous plant that comprises an R gene for a plant disease caused by at least one strain of PVY, at least one strain of PVA, and/or at least one potyvirus, the method comprising detecting in the plant, or in at least one part or cell thereof, the presence of: a c630 nucleotide sequence, a c516 nucleotide sequence, or a c630 nucleotide sequence and a c516 nucleotide sequence.
 2. The method of claim 1, wherein the solanaceous plant comprises enhanced resistance to at plant disease(s) caused by at least two strains of PVY and/or PVA.
 3. The method of claim 1, wherein the presence of the c630 nucleotide sequence is detected by detecting at least one marker within the c630 nucleotide sequence and wherein the presence of the c516 nucleotide sequence is detected by detecting at least one marker within the c516 nucleotide sequence.
 4. The method of claim 1, wherein the c630 nucleotide sequence comprises or consists of the nucleotide sequence set forth in SEQ ID NO:
 1. 5. The method of claim 1, wherein the c516 nucleotide sequence comprises or consists of the nucleotide sequence set forth in SEQ ID NO:
 6. 6. The method of claim 1, wherein detecting the presence of the c630 and/or c516 nucleotide sequence comprises a member selected from the group consisting of PCR amplification, nucleic acid sequencing, nucleic acid hybridization, and an immunological assay for the detection of (i) either one or both of the R proteins encoded by the c630 nucleotide sequence and/or (ii) the R protein encoded by the c516 nucleotide sequence.
 7. The method of claim 1, wherein detecting the presence of the c630 and/or c516 nucleotide sequence comprises PCR amplification.
 8. The method of claim 1, wherein detecting the presence of the c630 and/or c516 nucleotide sequence comprises nucleic acid sequencing.
 9. A method for introducing c630 and/or c516 into a solanaceous plant, the method comprising: (a) crossing a first solanaceous plant comprising in its genome at least one copy of c630, c516, or both c630 and c516, with a second solanaceous plant lacking in its genome c630, c516, or both c630 and c516, respectively, whereby at least one progeny plant is produced; and (b) selecting at least one progeny plant comprising in its genome c630, c516, or both c630 and c516 by detecting in the progeny plant the presence of c630, c516, or both c630 and c516, respectively.
 10. The method of claim 9, wherein the first solanaceous plant is a S. stoloniferum plant or a S. tuberosum plant and the second solanaceous plant is S. tuberosum plant lacking in its genome c630 and/or c516.
 11. The method of claim 9, wherein the presence of the c630 nucleotide sequence is detected by detecting at least one marker within the c630 nucleotide sequence and wherein the presence of the c516 nucleotide sequence is detected by detecting at least one marker within the c516 nucleotide sequence.
 12. The method of claim 9, wherein the c630 nucleotide sequence comprises or consists of the nucleotide sequence set forth in SEQ ID NO:
 1. 13. The method of claim 9, wherein the c516 nucleotide sequence comprises or consists of the nucleotide sequence set forth in SEQ ID NO:
 6. 14. The method of claim 9, wherein detecting the presence of the c630 and/or c516 nucleotide sequence comprises a member selected from the group consisting of PCR amplification, nucleic acid sequencing, nucleic acid hybridization, and an immunological assay for the detection of (i) either one or both of the R proteins encoded by the c630 nucleotide sequence and/or (ii) the R protein encoded by the c516 nucleotide sequence.
 15. The method of claim 9, wherein detecting the presence of the c630 and/or c516 nucleotide sequence comprises PCR amplification.
 16. The method of claim 9, wherein detecting the presence of the c630 and/or c516 nucleotide sequence comprises nucleic acid sequencing. 